I am going through the tutorial of DESEQ2 published on F1000. In the step of rlog transformation I have done following operation:
dds <- DESeqDataSet(se, design = ~cell + dex) dds <- dds[rowSums(counts(dds))>1,] f1<- plot(log2(counts(dds, normalized=FALSE)[,1:2] + 1), pch=16, cex=0.3) dds <- estimateSizeFactors(dds) f2 <- plot(log2(counts(dds, normalized=TRUE)[, 1:2] + 1), pch=16, cex=0.3) all(f1 ==f2)
And the result is:
> all(f1 ==f2)  TRUE
In this case, what is the point of "normalization" here? I know this might not related to the tutorial, but i am eager to get understand what each step means, any answer is appreciated!