Geez, I forgot it. Thanks a lot!!




________________________________
 From: Mark Robinson <mark.robinson@imls.uzh.ch>

Cc: "Bioconductor@r-project.org" <Bioconductor@r-project.org> 
Sent: Tuesday, March 19, 2013 4:48 PM
Subject: Re: [BioC] edgeR strange normalized factor for RNAseq data

Hi Caprice,

Probably you also want to run:

y <- calcNormFactors(y)

… then have a look at y$samples … 

Best, Mark





> I have 18 RNAseq libraries for 9 samples in duplicate. When I generated edgeR object, I found all the norm.factors are 1 even though the library size are so different. Could anyone please explain this for me and let me know if it is correct? Thanks.
> 
> Here are the code some results:
> 
>> group=factor(substring(names, 1,2))
>> group
>  [1] MP FA FR FW MA FW MM FP MA MW FM MM MW MP MM FP FA FR
> Levels: FA FM FP FR FW MA MM MP MW
>> design=model.matrix(~0+group)
>> y=DGEList(counts=data.used, group=group)
> Calculating library sizes from column totals.
>> y
> An object of class "DGEList"
> $counts
>           MP  FA  FR FW  MA FW.1  MM  FP MA.1  MW  FM MM.1 MW.1 MP.1 MM.2 FP.1
> GS_14929 221 284 170 23 267  105 209 106   52 218 158  277  170  926  185  211
> GS_09776  75  32  17 28  41   96  86  15   23  65  23   27   65   73   87   85
> GS_18434  36  22  19  8  21    6  22   7    7  27  13    6   21    2   23   15
> GS_08334  44  77  23 50  41   78  78  14   21  61  29    8   46   59   94  132
> GS_09550  82  92  45 54 105   75  95  18   79 153  41    8  111   11   86  178
>          FA.1 FR.1
> GS_14929  159    0
> GS_09776   52  143
> GS_18434   14   23
> GS_08334   92   60
> GS_09550   97   39
> 15457 more rows ...
> 
> $samples
>    group lib.size norm.factors
> MP    MP  2220863            1
> FA    FA  2179157            1
> FR    FR  1181036            1
> FW    FW  1305802            1
> MA    MA  1780507            1
> 13 more rows ...
> 
>> y$samples
>      group lib.size norm.factors
> MP      MP  2220863            1
> FA      FA  2179157            1
> FR      FR  1181036            1
> FW      FW  1305802            1
> MA      MA  1780507            1
> FW.1    FW  3388037            1
> MM      MM  2564495            1
> FP      FP   749402            1
> MA.1    MA  1299287            1
> MW      MW  2579787            1
> FM      FM  1355962            1
> MM.1    MM   867100            1
> MW.1    MW  2581031            1
> MP.1    MP  2115532            1
> MM.2    MM  2869116            1
> FP.1    FP  3112223            1
> FA.1    FA  2715113            1
> FR.1    FR  2770152            1
> -------------------------
> Here I can see, MP lib.size is 2220863, wherease FP lib.size is only 749402, but both norm.factors are 1
> 
> I am very confused...
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> 
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