[BioC] re incomplete analysis in Deseq
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Tue Mar 6 22:01:39 CET 2012
On Tue, Mar 6, 2012 at 3:28 PM, Wolfgang Huber <whuber at embl.de> wrote:
>
> 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'?
Hey, I am just reporting.
It might be worthwhile adding some check in
estimateSizeFactorsForMatrix to at least warn about the case where the
number of non-infinity rows is small, say less than 100. This could
be an issue with data types where the number of features is small, eg.
small RNAs or other types. I am sure people are using DESeq for these
types as well.
Kasper
>
> 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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