[BioC] re incomplete analysis in Deseq

Tue Mar 6 15:25:29 CET 2012

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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