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Hi:

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)
[1] 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!

Thank you for the answer. Does plot() equal mean the input is equal?

(I use == to test is because i see the image looks same)

No.

These aren't really questions related to Bioconductor software though, which is the purpose of this site, so you may want to look up some help on use of R for data analysis.

Thank you so much for kind answer.

Thank you so much for kind answer.