[BioC] DESeq cuont table normalization

[Wolfgang Huber]

Dear Fatemehsadat

thanks. This is an R question, not a specific question for DESeq. R is a 
functional language, in which (ideally) function calls such as the one 
you make below do not modify their argument in place. You can proceed 
with the DESeq vignette without worrying about your observation.

In addition, it might be a good idea to spend a little time 
familiarising yourself with the R language before jumping in the deep 
end. E.g. the excellent 'Introduction to R' that ships together with R, or
http://www.bioconductor.org/help/course-materials/2012/Bressanone2012/ 
-->  2012-07-02-Gatto-R-Basics.pdf

	Best wishes
	Wolfgang


On 9/19/12 11:22 AM, Fatemehsadat Seyednasrollah wrote:
> Hello,
>
> I am following the DESeq vignette and repeating what is mentioned there for my dataset.
> There is a step in the vignette which tries to normalize the count table to gain a common scale :
>> head( counts( cds, normalized=TRUE ) )
>
> When I run this line and then agin run the command :
> head(counts(cds))
>
> I see the amount of reads before normalization. Should not it change to the new amounts I mean the normalized amounts?
>
>
>> print (head(counts(mine, normalized = TRUE)))
>                    X3        X5          X4       X4.1        X2       X3.1
> A1BG     186.0036964 96.798204 231.6504223 90.4352020 92.027309  40.852657
> A1BG-AS1  22.3204436 29.143545  15.0666941 28.3718281 18.191445   8.881012
> A1CF       0.9300185  1.040841   0.9416684  1.7732393  1.070085   0.000000
> A2LD1     93.0018482 73.899704  92.2835016 86.0021039 63.135014 113.676959
> A2M        4.6500924  5.204205  21.6583728  0.8866196  5.350425   5.328607
> A2ML1      0.0000000  0.000000   0.0000000  0.0000000  0.000000   1.776202
>                  X1       X1.1
> A1BG      66.40690  90.562533
> A1BG-AS1  21.75399  14.916182
> A1CF       0.00000   1.065442
> A2LD1    100.75530 121.460339
> A2M       11.44947   5.327208
> A2ML1      0.00000   0.000000
>
>
>> head(counts(mine))
>            X3 X5  X4 X4.1 X2 X3.1 X1 X1.1
> A1BG     200 93 246  102 86   46 58   85
> A1BG-AS1  24 28  16   32 17   10 19   14
> A1CF       1  1   1    2  1    0  0    1
> A2LD1    100 71  98   97 59  128 88  114
> A2M        5  5  23    1  5    6 10    5
> A2ML1      0  0   0    0  0    2  0    0
>
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Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber