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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber