[BioC] Using Limma for proteomics (2D DIGE) datasets

Tom Wenseleers tom.wenseleers at bio.kuleuven.be
Sun Oct 18 14:05:07 CEST 2009


Dear all,
I am interested in using Limma/LimmaGUI for the analysis of 
proteomics (2D DIGE) datasets. I have had a try with LimmaGUI, 
however, I seem to keep on getting the message "limmaGUI was unable 
to read in the gene list from the raw (image analysis) files." 
(although the Cy3 and Cy5 data are read in fine) - any idea what I 
could be doing wrong? Main thing is I don't know how I should call 
the gene (well protein) list column... I attach a couple of the .spot 
files and the targets file for your info. I chose 
File...New...selected my targets file, then Type of Image processing 
file...Other Red foreground: Cy5, Red background: Cy5_b (I just put 
in zeros - hope that is OK?), Green foreground: Cy3, Green background: Cy3_b.
I have the latest Windows version of R and all the bioconductor 
packages installed. (Incidentally, during installation it complained 
about the sma package not being there - that appears to be no longer 
supported - but is still used in e.g. Limma, so this I guess needs 
sorting out - I installed an older archived version).

In proteomics we also have the Cy2 channel which is an internal 
control based on a pooled sample that is identical for all gels - but 
I think I do not have to use that since I am interested in the 
Cy3/Cy5 Log ratios and (Cy3/Cy2) / (Cy5/Cy2)=Cy3/Cy5, ie I think the 
Cy2 channel would only introduce additional noise.

Anyway if any of you would have experience in using Limma for the 
analysis of proteomics datasets, please let me know... Right now in 
the proteomics community people are mostly using simple t-tests etc, 
but using moderated t statistics would obviously be much better...
Maybe there would be some scope for writing a dedicated Bioconductor 
package for the analysis of proteomics 2D DIGE data, based on Limma 
or LimmaGUI, I don't know... I think most of the code would hardly 
need any changing, only the input of the data would need changing and 
maybe dealing with missing values could be better too (which is more 
of an issue in proteomics than in microarrays) (eg using a few 
preprocessing and analysis options, such as to leave them out, 
substitute by 0 or impute missing values using k nearest neighbours). 
I think this could greatly benefit the proteomics community.

cheers,
Tom Wenseleers


Dr. T. Wenseleers
Dept. of Biology
Zoological Institute
K.U.Leuven
Naamsestraat 59
B-3000 Leuven
Belgium
tel. +32 (0)16 32 39 64
mobile +32 (0)472 40 45 96
e-mail tom.wenseleers at bio.kuleuven.be
web http://bio.kuleuven.be/ento/wenseleers/twenseleers.htm  
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SlideNumber	Name	FileName	Cy3	Cy5
1	56_g1	brain_56_g1.spot	V	O
2	56_g2	brain_56_g2.spot	V	O
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1939	p1939	113085	125578	0	0
1940	p1940	908389	909127	0	0
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1943	p1943	696411	718469	0	0
1944	p1944	961425	1076525	0	0
1945	p1945	712938	731495	0	0
1946	p1946			0	0
1947	p1947	25288	6906	0	0
1948	p1948	90791	85337	0	0
1949	p1949	102534	74636	0	0
1950	p1950	41031	44540	0	0
1951	p1951	362420	408536	0	0
1952	p1952	234768	290597	0	0
1953	p1953	2125719	2495401	0	0
1954	p1954	60833	50341	0	0
1955	p1955	219745	241656	0	0
1956	p1956	97748	99345	0	0
1957	p1957			0	0
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1960	p1960			0	0
1961	p1961	313510	327512	0	0
1962	p1962	156263	212008	0	0
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1970	p1970			0	0
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1972	p1972	12643	26553	0	0
1973	p1973			0	0
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1975	p1975			0	0
1976	p1976			0	0
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1978	p1978	126299	124705	0	0
1979	p1979	150420	143308	0	0
1980	p1980			0	0
1981	p1981	1224156	1173858	0	0
1982	p1982	288534	282151	0	0
1983	p1983			0	0
1984	p1984			0	0
1985	p1985			0	0
1986	p1986	744815	770773	0	0
1987	p1987	283773	356968	0	0
1988	p1988	4931993	4504162	0	0
1989	p1989	2213690	2016761	0	0
1990	p1990	433528	462862	0	0
1991	p1991	443049	474316	0	0
1992	p1992	417282	410793	0	0
1993	p1993	341781	349590	0	0
1994	p1994			0	0
1995	p1995	10948210	843391	0	0
1996	p1996	7310006	523912	0	0
1997	p1997	138422	193906	0	0
1998	p1998	238236	228512	0	0
1999	p1999			0	0
2000	p2000	796669	1037078	0	0
2001	p2001			0	0
2002	p2002	4867	2242	0	0
2003	p2003			0	0
2004	p2004	90673	104475	0	0
2005	p2005	96768	96344	0	0
2006	p2006			0	0
2007	p2007	217880	218961	0	0
2008	p2008	90106	105881	0	0
2009	p2009	584366	563861	0	0
2010	p2010	101275	111436	0	0
2011	p2011	127987	127891	0	0
2012	p2012	45385	38552	0	0
2013	p2013	89650	105701	0	0
2014	p2014	2506729	2812567	0	0
2015	p2015			0	0
2016	p2016	33596	30980	0	0
2017	p2017			0	0
2018	p2018	12529118	930464	0	0
2019	p2019	290380	336253	0	0
2020	p2020	194017	214449	0	0
2021	p2021	886931	1012974	0	0
2022	p2022	864011	787381	0	0
2023	p2023	23299	6301	0	0
2024	p2024			0	0
2025	p2025			0	0
2026	p2026	651359	688623	0	0
2027	p2027	172104	169887	0	0
2028	p2028	586407	587957	0	0
2029	p2029	248268	238466	0	0
2030	p2030	313478	348222	0	0
2031	p2031	1058114	73753	0	0
2032	p2032			0	0
2033	p2033	67152	63644	0	0
2034	p2034			0	0
2035	p2035	592758	682048	0	0
2036	p2036	663510	699423	0	0
2037	p2037	44159	55515	0	0
2038	p2038	52077	42273	0	0
2039	p2039	36254	40248	0	0
2040	p2040			0	0
2041	p2041			0	0
2042	p2042	213887	318107	0	0
2043	p2043	154791	144781	0	0
2044	p2044	39130	36058	0	0
2045	p2045			0	0
2046	p2046	97365	113195	0	0
2047	p2047	345494	348741	0	0
2048	p2048	14118	15381	0	0
2049	p2049			0	0
2050	p2050			0	0
2051	p2051			0	0
2052	p2052	6070392	6123567	0	0
2053	p2053	91048	110436	0	0
2054	p2054	841184	809610	0	0
2055	p2055			0	0
2056	p2056	386236	401428	0	0
2057	p2057			0	0
2058	p2058			0	0
2059	p2059	275241	243395	0	0
2060	p2060	1235733	1400884	0	0
2061	p2061	155763	150694	0	0
2062	p2062	351911	374810	0	0
2063	p2063			0	0
2064	p2064	201411	195500	0	0
2065	p2065			0	0
2066	p2066			0	0
2067	p2067			0	0
2068	p2068	14634016	1086218	0	0
2069	p2069			0	0
2070	p2070	529957	482202	0	0
2071	p2071	65063	75402	0	0
2072	p2072			0	0
2073	p2073	113072	171784	0	0
2074	p2074			0	0
2075	p2075			0	0
2076	p2076	62410	61911	0	0
2077	p2077	116692	125352	0	0
2078	p2078	711034	660204	0	0
2079	p2079			0	0
2080	p2080	79816	94878	0	0
2081	p2081	63272	63818	0	0
2082	p2082	21300	7034	0	0
2083	p2083	58547	63531	0	0
2084	p2084	251312	279925	0	0
2085	p2085	28900	26350	0	0
2086	p2086	11312514	762565	0	0
2087	p2087			0	0
2088	p2088			0	0
2089	p2089	428156	522428	0	0
2090	p2090	236480	209760	0	0
2091	p2091			0	0
2092	p2092	369825	380398	0	0
2093	p2093	304759	289728	0	0
2094	p2094	70012	64650	0	0
2095	p2095			0	0
2096	p2096	154548	154537	0	0
2097	p2097	12328572	941259	0	0
2098	p2098	290950	295816	0	0
2099	p2099	92089	95266	0	0
2100	p2100	979045	974722	0	0
2101	p2101	140321	117071	0	0
2102	p2102	90252	103330	0	0
2103	p2103	1338496	1354304	0	0
2104	p2104			0	0
2105	p2105	525332	522066	0	0
2106	p2106			0	0
2107	p2107			0	0
2108	p2108	98492	89649	0	0
2109	p2109	113761	116619	0	0
2110	p2110	30233	25144	0	0
2111	p2111			0	0
2112	p2112			0	0
2113	p2113	34580	28415	0	0
2114	p2114			0	0
2115	p2115	10835	2822	0	0
2116	p2116	97474	217633	0	0
2117	p2117	2055641	1761881	0	0
2118	p2118			0	0
2119	p2119	363543	340581	0	0
2120	p2120	144730	134250	0	0
2121	p2121	248589	195491	0	0
2122	p2122			0	0
2123	p2123	263875	290116	0	0
2124	p2124			0	0
2125	p2125	37633	34656	0	0
2126	p2126	605767	593659	0	0
2127	p2127			0	0
2128	p2128	369481	317077	0	0
2129	p2129	63818	23178	0	0
2130	p2130			0	0
2131	p2131	146051	122245	0	0
2132	p2132	6560	1213	0	0
2133	p2133	75480	76066	0	0
2134	p2134	66747	49748	0	0
2135	p2135			0	0
2136	p2136	29786	28868	0	0
2137	p2137			0	0
2138	p2138			0	0
2139	p2139	15219	4439	0	0
2140	p2140	15019	2979	0	0
2141	p2141			0	0
2142	p2142			0	0
2143	p2143	321019	436325	0	0
2144	p2144			0	0
2145	p2145			0	0
2146	p2146	5198707	5143921	0	0
2147	p2147	16249	2709	0	0
2148	p2148			0	0
2149	p2149	897684	872588	0	0
2150	p2150	66814	110526	0	0
2151	p2151	76970	75802	0	0
2152	p2152	152482	212546	0	0
2153	p2153	53738	58608	0	0
2154	p2154	4729	2369	0	0
2155	p2155	186101	184949	0	0
2156	p2156			0	0
2157	p2157	59964	84215	0	0
2158	p2158			0	0
2159	p2159	290835	281638	0	0
2160	p2160			0	0
2161	p2161	35643	45539	0	0
2162	p2162	270864	288026	0	0
2163	p2163	5148	1263	0	0
2164	p2164	146890	125226	0	0
2165	p2165	77688	67986	0	0
2166	p2166			0	0
2167	p2167	114922	117367	0	0
2168	p2168	83362	85133	0	0
2169	p2169			0	0
2170	p2170	277118	259309	0	0
2171	p2171	65862	72425	0	0
2172	p2172	768408	700347	0	0
2173	p2173	85047	75385	0	0
2174	p2174			0	0
2175	p2175	228636	216366	0	0
2176	p2176			0	0
2177	p2177	31840	35464	0	0
2178	p2178			0	0
2179	p2179			0	0
2180	p2180	6850	3336	0	0
2181	p2181	9788	2104	0	0
2182	p2182	66334	101276	0	0
2183	p2183	361909	353368	0	0
2184	p2184			0	0
2185	p2185	47263	4612	0	0
2186	p2186			0	0
2187	p2187			0	0
2188	p2188	27620	28658	0	0
2189	p2189	777092	682508	0	0
2190	p2190	995165	943997	0	0
2191	p2191	78545	88051	0	0
2192	p2192	115389	66960	0	0
2193	p2193	55941	42334	0	0
2194	p2194	139508	139570	0	0
2195	p2195	101517	117568	0	0
2196	p2196	112521	92879	0	0
2197	p2197	78241	77056	0	0
2198	p2198	148577	158145	0	0
2199	p2199	261591	275340	0	0
2200	p2200	61792	82080	0	0
2201	p2201			0	0
2202	p2202			0	0
2203	p2203	290170	326514	0	0
2204	p2204	83393	87536	0	0
2205	p2205			0	0
2206	p2206	118719	150097	0	0
2207	p2207			0	0
2208	p2208	1206600	1325939	0	0
2209	p2209	1959763	1847187	0	0
2210	p2210			0	0
2211	p2211	14740	13351	0	0
2212	p2212	64296	68644	0	0
2213	p2213	256214	276090	0	0
2214	p2214	23014	30908	0	0
2215	p2215	51347	53397	0	0
2216	p2216			0	0
2217	p2217			0	0
2218	p2218	170840	149325	0	0
2219	p2219	31066	37598	0	0
2220	p2220	69294	83090	0	0
2221	p2221	71033	76872	0	0
2222	p2222	234152	243278	0	0
2223	p2223	141299	130667	0	0
2224	p2224	96733	96509	0	0
2225	p2225	854381	878485	0	0
2226	p2226	199532	203417	0	0
2227	p2227	58454	68899	0	0
2228	p2228	150493	163896	0	0
2229	p2229			0	0
2230	p2230	335303	360691	0	0
2231	p2231	71393	87413	0	0
2232	p2232	286481	182086	0	0
2233	p2233	10062	6374	0	0
2234	p2234	263935	410302	0	0
2235	p2235			0	0
2236	p2236	63339	59803	0	0
2237	p2237			0	0
2238	p2238	107829	127814	0	0
2239	p2239	61305	64204	0	0
2240	p2240			0	0
2241	p2241			0	0
2242	p2242	43356	37326	0	0
2243	p2243	745823	817879	0	0
2244	p2244			0	0
2245	p2245			0	0
2246	p2246	49393	34561	0	0
2247	p2247	72640	99238	0	0
2248	p2248	62537	102480	0	0
2249	p2249			0	0
2250	p2250	10895	2989	0	0
2251	p2251	16248	7005	0	0
2252	p2252	163982	164265	0	0
2253	p2253			0	0
2254	p2254			0	0
2255	p2255			0	0
2256	p2256	98901	112768	0	0
2257	p2257	51471	55967	0	0
2258	p2258			0	0
2259	p2259	93775	104042	0	0
2260	p2260	108283	121855	0	0
2261	p2261	90916	288365	0	0
2262	p2262	52791	58521	0	0
2263	p2263			0	0
2264	p2264	85255	99671	0	0
2265	p2265			0	0
2266	p2266	215873	228974	0	0
2267	p2267	197699	257213	0	0
2268	p2268	103451	953211	0	0
2269	p2269			0	0
2270	p2270	222466	215972	0	0
2271	p2271	397971	373607	0	0
2272	p2272	113450	126738	0	0
2273	p2273			0	0
2274	p2274	193494	179155	0	0
2275	p2275	196698	220289	0	0
2276	p2276			0	0
2277	p2277	288615	307241	0	0
2278	p2278	53239	97597	0	0
2279	p2279	504030	602191	0	0
2280	p2280			0	0
2281	p2281	97250	111630	0	0
2282	p2282			0	0
2283	p2283	65658	62693	0	0
2284	p2284	101365	102100	0	0
2285	p2285	228414	229224	0	0
2286	p2286			0	0
2287	p2287			0	0
2288	p2288	462221	513216	0	0
2289	p2289			0	0
2290	p2290			0	0
2291	p2291	152880	163424	0	0
2292	p2292			0	0
2293	p2293	36858	27821	0	0
2294	p2294	283619	283637	0	0
2295	p2295	391484	403776	0	0
2296	p2296	309858	308329	0	0
2297	p2297	387293	374066	0	0
2298	p2298			0	0
2299	p2299	32306	45702	0	0
2300	p2300			0	0
2301	p2301	116708	137082	0	0
2302	p2302	657465	698981	0	0
2303	p2303	136688	129423	0	0
2304	p2304	594146	629669	0	0
2305	p2305	40097383	38460005	0	0
2306	p2306	257986	340506	0	0
2307	p2307	6438727	5862173	0	0
2308	p2308			0	0
2309	p2309	186323	201182	0	0
2310	p2310	70115	61113	0	0
2311	p2311	59112	86733	0	0
2312	p2312	211023	196234	0	0
2313	p2313	369542	387207	0	0
2314	p2314	1010614	973503	0	0
2315	p2315	74738	69356	0	0
2316	p2316			0	0
2317	p2317	1702817	1659227	0	0
2318	p2318			0	0
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2320	p2320	218582	222153	0	0
2321	p2321	251953	275260	0	0
2322	p2322	75774	176723	0	0
2323	p2323	29395	77431	0	0
2324	p2324			0	0
2325	p2325	414588	421135	0	0
2326	p2326	336748	304760	0	0
2327	p2327	503923	429966	0	0
2328	p2328	216017	204559	0	0
2329	p2329	76615	70559	0	0
2330	p2330	92485	729088	0	0
2331	p2331			0	0
2332	p2332	382724	362691	0	0
2333	p2333	143800	134955	0	0
2334	p2334	24898	90505	0	0
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2949	p2949			0	0
2950	p2950	68664	73191	0	0
2951	p2951	107600	121738	0	0
2952	p2952			0	0
2953	p2953	72324	94373	0	0
2954	p2954			0	0
2955	p2955	11318	3109	0	0
2956	p2956			0	0
2957	p2957			0	0
2958	p2958			0	0
2959	p2959	618386	718605	0	0
2960	p2960	11290	2501	0	0
2961	p2961	31630	36312	0	0
2962	p2962			0	0
2963	p2963	24952	26787	0	0
2964	p2964			0	0
2965	p2965			0	0
2966	p2966	48218	50073	0	0
2967	p2967			0	0
2968	p2968			0	0
2969	p2969	867026	827662	0	0
2970	p2970			0	0
2971	p2971	195524	158471	0	0
2972	p2972			0	0
2973	p2973			0	0
2974	p2974			0	0
2975	p2975	24971	21529	0	0
2976	p2976			0	0
2977	p2977			0	0
2978	p2978	29503	29566	0	0
2979	p2979			0	0
2980	p2980	41125	8003	0	0
2981	p2981			0	0
2982	p2982			0	0
2983	p2983			0	0
2984	p2984			0	0
2985	p2985	34299	30468	0	0
2986	p2986			0	0
2987	p2987	9353	2848	0	0
2988	p2988			0	0
2989	p2989	67832	41978	0	0
2990	p2990	81936	82181	0	0
2991	p2991	63073	62080	0	0
2992	p2992			0	0
2993	p2993			0	0
2994	p2994	1587420	1268834	0	0
2995	p2995	98246	91288	0	0
2996	p2996	42988	44990	0	0
2997	p2997			0	0
2998	p2998	33321	17112	0	0
2999	p2999			0	0
3000	p3000			0	0
3001	p3001			0	0
3002	p3002	737525	756315	0	0
3003	p3003			0	0
3004	p3004	55975	56761	0	0
3005	p3005	137653	113154	0	0
3006	p3006			0	0
3007	p3007	34803	13978	0	0
3008	p3008	241401	267818	0	0
3009	p3009			0	0
3010	p3010			0	0
3011	p3011			0	0
3012	p3012	99160	120573	0	0
3013	p3013	267971	297309	0	0
3014	p3014	440891	513574	0	0
3015	p3015	39579	32088	0	0
3016	p3016	608149	706453	0	0
3017	p3017			0	0
3018	p3018	32866	20333	0	0
3019	p3019	12333	2624	0	0
3020	p3020	10013	2345	0	0
3021	p3021	52637	73148	0	0
3022	p3022			0	0
3023	p3023	37269	29983	0	0
3024	p3024			0	0
3025	p3025			0	0
3026	p3026	16754	24338	0	0
3027	p3027			0	0
3028	p3028	287336	333381	0	0
3029	p3029			0	0
3030	p3030			0	0
3031	p3031			0	0
3032	p3032			0	0
3033	p3033			0	0
3034	p3034			0	0
3035	p3035	17995	17542	0	0
3036	p3036	89122	40012	0	0
3037	p3037	9463	2909	0	0
3038	p3038	145385	69502	0	0
3039	p3039	35933	26396	0	0
3040	p3040	81529	99626	0	0
3041	p3041	12249	15521	0	0
3042	p3042			0	0
3043	p3043			0	0
3044	p3044			0	0
3045	p3045			0	0
3046	p3046	55366	48765	0	0
3047	p3047			0	0
3048	p3048			0	0
3049	p3049			0	0
3050	p3050	453576	386357	0	0
3051	p3051			0	0
3052	p3052			0	0
3053	p3053	45686	57232	0	0
3054	p3054			0	0
3055	p3055	404843	484560	0	0
3056	p3056			0	0
3057	p3057			0	0
3058	p3058			0	0
3059	p3059			0	0
3060	p3060	33007	8256	0	0
3061	p3061			0	0
3062	p3062			0	0
3063	p3063	20020	18883	0	0
3064	p3064			0	0
3065	p3065			0	0
3066	p3066			0	0
3067	p3067			0	0
3068	p3068	91148	43769	0	0
3069	p3069	110660	52797	0	0
3070	p3070			0	0
3071	p3071	54384	53164	0	0
3072	p3072			0	0
3073	p3073	364217	365207	0	0
3074	p3074	43934	39322	0	0
3075	p3075	113789	120506	0	0
3076	p3076	5804	2706	0	0
3077	p3077			0	0
3078	p3078			0	0
3079	p3079			0	0
3080	p3080	39913	33435	0	0
3081	p3081	110813	46816	0	0
3082	p3082			0	0
3083	p3083			0	0
3084	p3084	409484	430652	0	0
3085	p3085	141457	210513	0	0
3086	p3086	23780	32139	0	0
3087	p3087			0	0
3088	p3088			0	0
3089	p3089	34870	25167	0	0
3090	p3090			0	0
3091	p3091			0	0
3092	p3092	87769	105709	0	0
3093	p3093	23660	4474	0	0
3094	p3094			0	0
3095	p3095	126118	115474	0	0
3096	p3096			0	0
3097	p3097	10155	3442	0	0
3098	p3098	81708	60814	0	0
3099	p3099	48353	30014	0	0
3100	p3100			0	0
3101	p3101	22642	28106	0	0
3102	p3102			0	0
3103	p3103			0	0
3104	p3104	29614	35683	0	0
3105	p3105			0	0
3106	p3106			0	0
3107	p3107	60029	70754	0	0
3108	p3108			0	0
3109	p3109	7676	2483	0	0
3110	p3110			0	0
3111	p3111	19456	4986	0	0
3112	p3112	230412	259437	0	0
3113	p3113	26734	20861	0	0
3114	p3114			0	0
3115	p3115	103072	8011	0	0
3116	p3116			0	0
3117	p3117	84143	75359	0	0
3118	p3118			0	0
3119	p3119	53630	34013	0	0
3120	p3120	81870	110880	0	0
3121	p3121			0	0
3122	p3122			0	0
3123	p3123	46837	43844	0	0
3124	p3124			0	0
3125	p3125			0	0
3126	p3126	35596	38813	0	0
3127	p3127			0	0
3128	p3128			0	0
3129	p3129			0	0
3130	p3130	3838577	3942707	0	0
3131	p3131	159473	165635	0	0
3132	p3132			0	0
3133	p3133			0	0
3134	p3134			0	0
3135	p3135			0	0
3136	p3136			0	0
3137	p3137			0	0
3138	p3138			0	0
3139	p3139	9271	2469	0	0
3140	p3140	91352	87805	0	0
3141	p3141			0	0
3142	p3142	96330	53545	0	0
3143	p3143			0	0
3144	p3144			0	0
3145	p3145			0	0
3146	p3146			0	0
3147	p3147			0	0
3148	p3148			0	0
3149	p3149			0	0
3150	p3150			0	0
3151	p3151			0	0
3152	p3152			0	0
3153	p3153			0	0
3154	p3154			0	0
3155	p3155			0	0
3156	p3156			0	0
3157	p3157	80408	54837	0	0
3158	p3158			0	0
3159	p3159			0	0
3160	p3160			0	0
3161	p3161			0	0
3162	p3162			0	0
3163	p3163			0	0
3164	p3164			0	0
3165	p3165			0	0
3166	p3166			0	0
3167	p3167			0	0
3168	p3168			0	0
3169	p3169	54778	28347	0	0
3170	p3170			0	0
3171	p3171			0	0
3172	p3172			0	0
3173	p3173			0	0
3174	p3174			0	0
3175	p3175			0	0
3176	p3176			0	0
3177	p3177			0	0
3178	p3178			0	0
3179	p3179			0	0
3180	p3180			0	0
3181	p3181			0	0
3182	p3182			0	0
3183	p3183			0	0
3184	p3184			0	0
3185	p3185			0	0
3186	p3186			0	0
3187	p3187			0	0
3188	p3188			0	0
3189	p3189			0	0
3190	p3190			0	0
3191	p3191			0	0
3192	p3192			0	0
3193	p3193			0	0
3194	p3194			0	0
3195	p3195			0	0
3196	p3196			0	0
3197	p3197			0	0
3199	p3199			0	0
3200	p3200			0	0
3201	p3201			0	0
3202	p3202			0	0
3203	p3203			0	0
3204	p3204			0	0
3205	p3205			0	0
3206	p3206			0	0
3207	p3207			0	0
3208	p3208			0	0
3209	p3209			0	0
3210	p3210			0	0
3211	p3211			0	0
3212	p3212			0	0
3213	p3213			0	0
3214	p3214			0	0
3215	p3215			0	0
3216	p3216			0	0
3217	p3217			0	0
3218	p3218			0	0
3219	p3219			0	0
3220	p3220			0	0
3221	p3221			0	0
3222	p3222			0	0
3223	p3223			0	0
3224	p3224			0	0
3225	p3225			0	0
3226	p3226			0	0
3227	p3227			0	0
3228	p3228			0	0
3229	p3229			0	0
3230	p3230			0	0
3231	p3231			0	0
3232	p3232			0	0
3233	p3233			0	0
3234	p3234			0	0
3235	p3235			0	0
3236	p3236			0	0
3237	p3237			0	0
3238	p3238			0	0
3239	p3239			0	0
3241	p3241			0	0
3243	p3243			0	0
3244	p3244			0	0
3245	p3245			0	0
3246	p3246			0	0
3247	p3247			0	0
3249	p3249			0	0
3250	p3250			0	0
3251	p3251			0	0
3252	p3252			0	0
3253	p3253			0	0
3254	p3254			0	0
3255	p3255			0	0
3256	p3256			0	0
3258	p3258			0	0
3259	p3259			0	0
3260	p3260			0	0
3261	p3261			0	0
3262	p3262			0	0
3264	p3264			0	0
3265	p3265			0	0
3266	p3266			0	0
3267	p3267			0	0
3268	p3268			0	0
3269	p3269			0	0
3270	p3270			0	0
3271	p3271			0	0
3272	p3272			0	0
3273	p3273			0	0
3274	p3274			0	0
3275	p3275			0	0
3276	p3276			0	0
3278	p3278			0	0
3279	p3279			0	0
3280	p3280			0	0
3281	p3281			0	0
3282	p3282			0	0
3283	p3283			0	0
3285	p3285			0	0
3286	p3286			0	0
3287	p3287			0	0
3288	p3288			0	0
3289	p3289			0	0
3290	p3290			0	0
3291	p3291			0	0
3292	p3292			0	0
3293	p3293			0	0
3294	p3294			0	0
3295	p3295			0	0
3296	p3296			0	0
3297	p3297			0	0
3299	p3299			0	0
3300	p3300			0	0
3301	p3301			0	0
3302	p3302			0	0
3303	p3303			0	0
3305	p3305			0	0
3306	p3306			0	0
3307	p3307			0	0
3308	p3308			0	0
3309	p3309			0	0
3310	p3310			0	0
3311	p3311			0	0
3312	p3312			0	0
3313	p3313			0	0
3314	p3314			0	0
3315	p3315			0	0
3316	p3316			0	0
3317	p3317			0	0
3318	p3318			0	0
3319	p3319			0	0
3320	p3320			0	0
3321	p3321			0	0
3322	p3322			0	0
3323	p3323			0	0
3325	p3325			0	0
3326	p3326			0	0
3327	p3327			0	0
3329	p3329			0	0
3330	p3330			0	0
3331	p3331			0	0
3332	p3332			0	0
3333	p3333			0	0
3334	p3334			0	0
3335	p3335			0	0
3336	p3336			0	0
3337	p3337			0	0
3338	p3338			0	0
3339	p3339			0	0
3340	p3340			0	0
3341	p3341			0	0
3342	p3342			0	0
3344	p3344			0	0
3345	p3345			0	0
3346	p3346			0	0
3347	p3347			0	0
3348	p3348			0	0
3349	p3349			0	0
3350	p3350			0	0
3352	p3352			0	0
3353	p3353			0	0
3355	p3355			0	0
3357	p3357			0	0
3358	p3358			0	0
3359	p3359			0	0
3360	p3360			0	0
3361	p3361			0	0
3362	p3362			0	0
3363	p3363			0	0
3364	p3364			0	0
3365	p3365			0	0
3366	p3366			0	0
3367	p3367			0	0
3368	p3368			0	0
3371	p3371			0	0
3373	p3373			0	0
3374	p3374			0	0
3375	p3375			0	0
3376	p3376			0	0
3377	p3377			0	0
3378	p3378			0	0
3379	p3379			0	0
3380	p3380			0	0
3381	p3381			0	0
3384	p3384			0	0
-------------- next part --------------
row.names	genes	Cy3	Cy5	Cy3_b	Cy5_b
1	p1			0	0
2	p2			0	0
3	p3			0	0
4	p4			0	0
5	p5			0	0
8	p8			0	0
10	p10			0	0
11	p11			0	0
12	p12			0	0
13	p13			0	0
16	p16			0	0
18	p18			0	0
19	p19			0	0
22	p22			0	0
23	p23			0	0
24	p24			0	0
25	p25			0	0
26	p26			0	0
27	p27			0	0
28	p28			0	0
29	p29			0	0
30	p30			0	0
33	p33			0	0
34	p34			0	0
36	p36			0	0
38	p38			0	0
39	p39			0	0
40	p40			0	0
41	p41			0	0
42	p42			0	0
43	p43			0	0
45	p45			0	0
46	p46			0	0
47	p47			0	0
48	p48			0	0
51	p51			0	0
53	p53			0	0
55	p55			0	0
57	p57			0	0
58	p58			0	0
59	p59			0	0
60	p60			0	0
61	p61			0	0
62	p62			0	0
63	p63			0	0
64	p64			0	0
66	p66			0	0
67	p67			0	0
68	p68			0	0
69	p69			0	0
70	p70			0	0
71	p71			0	0
72	p72			0	0
73	p73			0	0
74	p74			0	0
75	p75			0	0
77	p77			0	0
78	p78			0	0
79	p79			0	0
80	p80			0	0
81	p81			0	0
82	p82			0	0
83	p83			0	0
84	p84			0	0
85	p85			0	0
86	p86			0	0
87	p87			0	0
88	p88			0	0
89	p89			0	0
90	p90			0	0
91	p91			0	0
92	p92			0	0
93	p93			0	0
94	p94			0	0
95	p95			0	0
96	p96			0	0
97	p97			0	0
98	p98			0	0
99	p99			0	0
100	p100			0	0
101	p101			0	0
103	p103			0	0
105	p105			0	0
107	p107			0	0
108	p108			0	0
110	p110			0	0
111	p111			0	0
112	p112			0	0
113	p113			0	0
115	p115			0	0
116	p116			0	0
119	p119			0	0
120	p120			0	0
122	p122			0	0
123	p123			0	0
124	p124			0	0
125	p125			0	0
126	p126			0	0
127	p127			0	0
128	p128			0	0
129	p129			0	0
130	p130			0	0
131	p131			0	0
132	p132			0	0
133	p133			0	0
134	p134			0	0
135	p135			0	0
136	p136			0	0
137	p137			0	0
138	p138			0	0
139	p139			0	0
140	p140			0	0
141	p141			0	0
144	p144			0	0
145	p145			0	0
146	p146			0	0
147	p147			0	0
148	p148			0	0
149	p149			0	0
150	p150			0	0
151	p151			0	0
155	p155			0	0
156	p156			0	0
157	p157			0	0
158	p158			0	0
159	p159			0	0
160	p160			0	0
161	p161			0	0
162	p162	2670743	2628705	0	0
163	p163			0	0
164	p164	2651499	2644432	0	0
165	p165			0	0
166	p166			0	0
167	p167			0	0
168	p168	2993256	3093478	0	0
169	p169			0	0
170	p170			0	0
171	p171	6710284	7683330	0	0
172	p172	556561	763610	0	0
173	p173			0	0
174	p174			0	0
175	p175			0	0
176	p176	161905	322296	0	0
177	p177			0	0
178	p178			0	0
179	p179			0	0
180	p180			0	0
181	p181	1913843	1989633	0	0
182	p182			0	0
183	p183	372753	442902	0	0
184	p184			0	0
185	p185			0	0
186	p186			0	0
187	p187			0	0
188	p188			0	0
189	p189	111086	129243	0	0
190	p190			0	0
191	p191			0	0
192	p192			0	0
193	p193			0	0
194	p194			0	0
195	p195			0	0
196	p196			0	0
197	p197			0	0
198	p198			0	0
199	p199			0	0
200	p200			0	0
201	p201			0	0
202	p202			0	0
203	p203	204067	301380	0	0
204	p204			0	0
205	p205			0	0
208	p208			0	0
209	p209			0	0
210	p210			0	0
211	p211			0	0
212	p212			0	0
213	p213	7773953	7169643	0	0
214	p214			0	0
215	p215	787728	2253628	0	0
216	p216			0	0
217	p217	480412	2092465	0	0
218	p218	104112	185095	0	0
219	p219	384279	519399	0	0
221	p221			0	0
222	p222			0	0
223	p223	425519	2248704	0	0
224	p224			0	0
225	p225	764341	900570	0	0
226	p226	517197	597459	0	0
227	p227			0	0
228	p228	100568	93619	0	0
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1701	p1701	1987742	891957	0	0
1702	p1702			0	0
1703	p1703	3277457	3602150	0	0
1704	p1704	160019	181519	0	0
1705	p1705			0	0
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1707	p1707	5360262	4255233	0	0
1708	p1708	10618195	8411276	0	0
1709	p1709	30882	20292	0	0
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1711	p1711	2333776	2851385	0	0
1712	p1712			0	0
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1714	p1714	1179839	1275967	0	0
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1729	p1729	78751	122046	0	0
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1799	p1799	519572	622699	0	0
1800	p1800	491954	586563	0	0
1801	p1801	201958	250060	0	0
1802	p1802	1057631	1118235	0	0
1803	p1803	558559	887301	0	0
1804	p1804	356788	395069	0	0
1805	p1805	772436	795810	0	0
1806	p1806	4703810	6415688	0	0
1807	p1807	36695	37724	0	0
1808	p1808	396073	717641	0	0
1809	p1809	3066118	1465206	0	0
1810	p1810			0	0
1811	p1811	1464738	1927853	0	0
1812	p1812	45202	58302	0	0
1813	p1813	1853608	4454892	0	0
1814	p1814	10933180	28157686	0	0
1815	p1815	363613	500162	0	0
1816	p1816			0	0
1817	p1817	585781	662720	0	0
1818	p1818	839790	1038533	0	0
1819	p1819	528228	573473	0	0
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1829	p1829	3608736	4515347	0	0
1830	p1830			0	0
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1832	p1832	144348	180347	0	0
1833	p1833	3283340	3293411	0	0
1834	p1834	1135550	1188743	0	0
1835	p1835	397675	459453	0	0
1836	p1836			0	0
1837	p1837	3184904	3034952	0	0
1838	p1838	18538	30504	0	0
1839	p1839	1418389	1204837	0	0
1840	p1840			0	0
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1842	p1842	1410176	1398933	0	0
1843	p1843	248735	294802	0	0
1844	p1844	626884	558609	0	0
1845	p1845	1401269	1473979	0	0
1846	p1846	394379	437615	0	0
1847	p1847	3498523	4047997	0	0
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1850	p1850	396523	499416	0	0
1851	p1851	99139	120682	0	0
1852	p1852	2722811	1956907	0	0
1853	p1853	1597156	1050239	0	0
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1855	p1855	14693444	9361957	0	0
1856	p1856			0	0
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1858	p1858	185691	297474	0	0
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1860	p1860	279264	439358	0	0
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1862	p1862	5093880	5144355	0	0
1863	p1863	2028814	2349063	0	0
1864	p1864			0	0
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1867	p1867	1252185	1457509	0	0
1868	p1868	298521	276756	0	0
1869	p1869	232618	271451	0	0
1870	p1870	143356	192510	0	0
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1873	p1873	60860	96065	0	0
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1876	p1876	50473	85138	0	0
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1878	p1878	27898	33423	0	0
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1880	p1880			0	0
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1883	p1883	94041	171946	0	0
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1887	p1887	32090	12427	0	0
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1891	p1891	202248	222351	0	0
1892	p1892			0	0
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1894	p1894	53798	73563	0	0
1895	p1895	58048	71018	0	0
1896	p1896	111455	140327	0	0
1897	p1897			0	0
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1899	p1899	126065	164803	0	0
1900	p1900	21992	11432	0	0
1901	p1901	126304	134489	0	0
1902	p1902			0	0
1903	p1903			0	0
1904	p1904	10976	3178	0	0
1905	p1905	8917	4934	0	0
1906	p1906	367557	404396	0	0
1907	p1907	802913	878533	0	0
1908	p1908	737093	890037	0	0
1909	p1909	186365	240349	0	0
1910	p1910	180412	214591	0	0
1911	p1911			0	0
1912	p1912	649908	616151	0	0
1913	p1913			0	0
1914	p1914	1050386	1726847	0	0
1915	p1915	231086	273698	0	0
1916	p1916	180202	207347	0	0
1917	p1917	435957	553289	0	0
1918	p1918			0	0
1919	p1919	3423640	2558607	0	0
1920	p1920	41488	54512	0	0
1921	p1921	206400	243405	0	0
1922	p1922	556690	737059	0	0
1923	p1923	1141648	1032862	0	0
1924	p1924	648326	536279	0	0
1925	p1925			0	0
1926	p1926	295891	330147	0	0
1927	p1927			0	0
1928	p1928			0	0
1929	p1929	307167	469829	0	0
1930	p1930	841557	1152793	0	0
1931	p1931	274126	337032	0	0
1932	p1932	215022	345681	0	0
1933	p1933			0	0
1934	p1934	102381	133669	0	0
1935	p1935			0	0
1936	p1936	213511	327413	0	0
1937	p1937	524368	712737	0	0
1938	p1938	920442	1256380	0	0
1939	p1939	244321	369547	0	0
1940	p1940	1294443	1494908	0	0
1941	p1941	15174556	14233837	0	0
1942	p1942	19071	5529	0	0
1943	p1943	529618	679491	0	0
1944	p1944	751948	1478410	0	0
1945	p1945	522407	658381	0	0
1946	p1946	14501	1889	0	0
1947	p1947			0	0
1948	p1948			0	0
1949	p1949			0	0
1950	p1950			0	0
1951	p1951	406510	299384	0	0
1952	p1952	190723	278441	0	0
1953	p1953	2039386	3839884	0	0
1954	p1954	96524	120720	0	0
1955	p1955	318055	364065	0	0
1956	p1956	33617	42831	0	0
1957	p1957	103395	167931	0	0
1958	p1958			0	0
1959	p1959	449560	639504	0	0
1960	p1960			0	0
1961	p1961	77231	86367	0	0
1962	p1962	465741	676239	0	0
1963	p1963	260736	268016	0	0
1964	p1964	541750	570176	0	0
1965	p1965	21210	8792	0	0
1966	p1966			0	0
1967	p1967	327309	319616	0	0
1968	p1968	2002044	2462551	0	0
1969	p1969	1468700	1761717	0	0
1970	p1970	104209	133742	0	0
1971	p1971			0	0
1972	p1972	14900	3295	0	0
1973	p1973			0	0
1974	p1974			0	0
1975	p1975	726800	1035202	0	0
1976	p1976	201267	264189	0	0
1977	p1977	165850	205131	0	0
1978	p1978	194169	217894	0	0
1979	p1979			0	0
1980	p1980	199301	290113	0	0
1981	p1981	1130235	1196646	0	0
1982	p1982			0	0
1983	p1983	32162	28942	0	0
1984	p1984			0	0
1985	p1985	1304131	1329377	0	0
1986	p1986	919162	1100047	0	0
1987	p1987	1150240	1579838	0	0
1988	p1988	6314880	6053639	0	0
1989	p1989	2942373	2928812	0	0
1990	p1990	490103	592794	0	0
1991	p1991			0	0
1992	p1992	395120	453216	0	0
1993	p1993	428816	529032	0	0
1994	p1994			0	0
1995	p1995	10164250	962935	0	0
1996	p1996	13529686	1277169	0	0
1997	p1997			0	0
1998	p1998	66671	73583	0	0
1999	p1999			0	0
2000	p2000	765668	1096834	0	0
2001	p2001			0	0
2002	p2002	4130	4482	0	0
2003	p2003			0	0
2004	p2004	253392	295416	0	0
2005	p2005			0	0
2006	p2006			0	0
2007	p2007	350686	404326	0	0
2008	p2008	89474	130084	0	0
2009	p2009	594571	643216	0	0
2010	p2010	67809	88482	0	0
2011	p2011	79495	94542	0	0
2012	p2012	204899	242097	0	0
2013	p2013			0	0
2014	p2014	2998788	3413011	0	0
2015	p2015	209319	234914	0	0
2016	p2016			0	0
2017	p2017	124101	176946	0	0
2018	p2018	15686217	1557267	0	0
2019	p2019			0	0
2020	p2020			0	0
2021	p2021			0	0
2022	p2022	987437	990992	0	0
2023	p2023	20813	6331	0	0
2024	p2024			0	0
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2027	p2027	306444	268050	0	0
2028	p2028	647405	752643	0	0
2029	p2029	554751	583045	0	0
2030	p2030	54114	65329	0	0
2031	p2031	1419282	96523	0	0
2032	p2032			0	0
2033	p2033	152715	159863	0	0
2034	p2034			0	0
2035	p2035			0	0
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2037	p2037			0	0
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2047	p2047	441883	482263	0	0
2048	p2048	19782	6475	0	0
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2051	p2051			0	0
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2054	p2054	953445	923556	0	0
2055	p2055	33005	43576	0	0
2056	p2056	524705	576953	0	0
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2060	p2060	1789945	1933683	0	0
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2062	p2062	606029	691555	0	0
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2076	p2076	48147	50124	0	0
2077	p2077	83874	75737	0	0
2078	p2078	869117	807079	0	0
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2087	p2087	8849	6680	0	0
2088	p2088	115660	115588	0	0
2089	p2089	490887	645257	0	0
2090	p2090			0	0
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2093	p2093	231191	217047	0	0
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2097	p2097	17228739	1793923	0	0
2098	p2098	6002304	5819647	0	0
2099	p2099	546395	619798	0	0
2100	p2100			0	0
2101	p2101	59204	70229	0	0
2102	p2102			0	0
2103	p2103	1949387	2268453	0	0
2104	p2104	82201	236758	0	0
2105	p2105			0	0
2106	p2106			0	0
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2109	p2109	124489	124194	0	0
2110	p2110			0	0
2111	p2111	17381	4857	0	0
2112	p2112	341843	450632	0	0
2113	p2113	65847	92541	0	0
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2116	p2116	59985	55749	0	0
2117	p2117	3138206	4050203	0	0
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2122	p2122			0	0
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2126	p2126	664730	763885	0	0
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2128	p2128	297794	383269	0	0
2129	p2129	43665	31441	0	0
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2178	p2178	381038	182481	0	0
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