Normalized Values from DESeq2

[TheSeqGeek]

This is the raw table example of my data but....

Gene Name Mutant Mutant Mutant WT WT WT
A 2343 2341 2842 1549 1303 1123

Can I get a table that has these normalized from DESeq2

[TheSeqGeek]

is this correct? or is this for the previous version of DESeq


normalizedCounts <- t( t(counts(dds)) / sizeFactors(dds) )

[dpryan]

counts(dds, normalized=T)

[TheSeqGeek]

counts(dds, normalized=T)

Thank you

Those two codes give the same results... Do you know why when I take the normalized to values and perform a log2fold change it is not the same as in DESeq2 log2foldchange


1.) take average of three replicates for mutant
2.) take average of three replicates for wt
3.) log2(mutatnt) - log2(wt)

This comes close to DESeq2 log2fold change but not quite the same...

[dpryan]

It'll be a little off due to fold-change shrinkage (i.e., your calculated values should generally be larger).

[TheSeqGeek]

It'll be a little off due to fold-change shrinkage (i.e., your calculated values should generally be larger).

Indeed that is the case.

Thank you