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Transform TMM value into log2(TMM) or rlog(TMM) in DESeq is OK?

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?

rna-seq
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written by xiaoxiaoxiaobu • xiaoxiaoxiaobu

Hi,

you can log2 transform your data and then do a PCA, but do not feed rlog() or vst() with TMM values

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written by andres.firrincieli andres.firrincieli

Thanks!

Indeed only count matrix is OK for rlog() or vst()!

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written by xiaoxiaoxiaobu • xiaoxiaoxiaobu

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