Entering edit mode
3.6 years ago
xiaoxiaoxiaobu
•
0
Hi everyone,
I got the TMM value for each gene of my 18 samples from Trinity pipeline and now wants to cluster or do the PCA analysis to them. However some of the genes have very large TMM value which could disturb the cluster as describle in DESeq2's manual Data transformations and visualization. So my question would be that if I could feed rlog() or vst() with my TMM vaule matrix, or simply using log2(TMM) to do cluster?
Hi,
you can
log2
transform your data and then do a PCA, but do not feedrlog()
orvst()
withTMM
valuesThanks!
Indeed only count matrix is OK for
rlog()
orvst()
!