[BioC] re incomplete analysis in Deseq
Wolfgang Huber
whuber at embl.de
Tue Mar 6 21:28:14 CET 2012
Hi Julian, Kasper
in this case you will need to (and as I am sure, be able to) come up
with another method for estimating size factors that works on these
data. Why not try with the 'colSums'?
Best wishes
Wolfgang
Mar/6/12 3:25 PM, Kasper Daniel Hansen scripsit::
> I got the data from Julian. It is not a standard RNA-seq experiment.
> He only has 150 "genes" (rows), but 76 samples (columns). There are
> no NA's. The problem arises from the fact that
> estimateSizeFactorsForMatrix only uses rows (genes) where all samples
> have counts> 0. In Julian's case, all rows have at least one column
> with zero counts, implying that loggeomeans is -Inf for all rows.
>
> Kasper
>
> On Mon, Mar 5, 2012 at 10:59 AM, Wolfgang Huber<whuber at embl.de> wrote:
>> Dear Julian
>>
>> do your data contain NA?
>> What is the output of sessionInfo()?
>>
>> Can you provide a code example (incl. input data, potentially subset) that
>> reproduces your error?
>>
>> Best wishes
>> Wolfgang
>>
>>
>> Mar/5/12 11:50 AM, Julian [guest] scripsit::
>>
>>>
>>> I'm using deseq with 454 data and it worked for one set of data but the
>>> same script is failing me the second time around with a different set of
>>> experimental data.
>>>
>>> The input data is a matrix of counts of 454 seqs per sample, I have 36 pre
>>> and 36 post samples.
>>>
>>> When I run the estmateSizeFactors I get all my samples as NA.
>>>
>>> Any ideas why?
>>>
>>> -- output of sessionInfo():
>>>
>>>
>>>> cds<- estimateSizeFactors(cds) # Estimates
>>>> size factors based on the count data
>>>> sizeFactors( cds )
>>>
>>> X01_MA_1 X02_MA_10 X03_MA_100 X04_MA_102 X05_MA_11 X06_MA_13
>>> X07_MA_14 X08_MA_15 X09_MA_17 X10_MA_18 X11_MA_19
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X12_MA_2 X13_MA_20 X14_MA_22 X15_MA_23 X16_MA_24 X17_MA_25
>>> X18_MA_4 X19_MA_47 X20_MA_5 X21_MA_69 X22_MA_7
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X23_MA_71 X24_MA_73 X25_MA_75 X26_MA_77 X27_MA_79 X28_MA_8
>>> X29_MA_81 X30_MA_83 X31_MA_86 X32_MA_88 X33_MA_9
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X34_MA_90 X35_MA_92 X36_MA_94 X37_MA_96 X38_MA_98 X39_MA_101
>>> X40_MA_103 X41_MA_26 X42_MA_27 X43_MA_29 X44_MA_30
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X45_MA_31 X46_MA_33 X47_MA_34 X48_MA_36 X49_MA_37 X50_MA_40
>>> X51_MA_41 X52_MA_42 X53_MA_43 X54_MA_44 X55_MA_45
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X56_MA_46 X57_MA_49 X58_MA_50 X59_MA_52 X60_MA_54 X61_MA_55
>>> X62_MA_70 X63_MA_72 X64_MA_74 X65_MA_76 X66_MA_78
>>> NA NA NA NA NA NA
>>> NA NA NA NA NA
>>> X67_MA_80 X68_MA_82 X69_MA_84 X70_MA_87 X71_MA_89 X72_MA_91
>>> X73_MA_93 X74_MA_95 X75_MA_97 X76_MA_99
>>> NA NA NA NA NA NA
>>> NA NA NA NA
>>>
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>>
>>
>> --
>> Best wishes
>> Wolfgang
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>>
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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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