[BioC] re incomplete analysis in Deseq
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Mon Mar 5 16:56:47 CET 2012
My guess is that you have NA's in your count matrix.
Kasper
On Mon, Mar 5, 2012 at 5:50 AM, Julian [guest] <guest at bioconductor.org> wrote:
>
> 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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