[BioC] re incomplete analysis in Deseq

[Wolfgang Huber]

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
>
>
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>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber