Question

To analyze the overall variance, which one to choose, vst or DESeq2 normalized counts?

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Raymond ▴ 20

@raymond-14020

Last seen 4.9 years ago

Hi, All,

I have two groups of RNAseq data, each group have 5 samples. I suspected that drug treatment would increase the overall expression variances in some pathways. So, I planned to compare all gene expression variances in that pathway or even in the top 500 expressed genes. I could calculate the variance from DEseq2 normalized counts, or variance stabilization transformed counts (vst or rld). The question is: which one should I choose? Does the VST process affect the signal I want to analyze?

Thanks and best regards,

Raymond

deseq2 • 1.7k views

ADD COMMENT • link updated 6.2 years ago by Alan ▴ 10 • written 6.2 years ago by Raymond ▴ 20

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Hi Michael,

May I ask:

1) Could you specify a little bit more about what are the some of reasons for favoring VST over rlog?

2) To clarify, the VST procedure is just for purpose of clustering and visualization, right? It (the counts after VST) basically is not involved in testing for pairwise DE with the Wald test?

Thank you very much in advance.

ADD REPLY • link 6.2 years ago Alan ▴ 10

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Please check out the vignette and workflow sections on transformations. We cover both of these questions there.

ADD REPLY • link 6.2 years ago Michael Love 41k

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OK I see, thank you, Michael.

ADD REPLY • link 6.2 years ago Alan ▴ 10

score 1 · Answer 1 · 2018-02-20

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Michael Love 41k

@mikelove

Last seen 1 day ago

United States

I recommend the vst(). It will help you compare variances across genes. You could also use rlog() I just prefer vst() these days.

ADD COMMENT • link 6.2 years ago Michael Love 41k

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Thanks so much, Michael! For 'across genes', do you mean the variances of genes in the same group? I want to compare the variances of the same genes between different groups. In this case, dose vst also help?

ADD REPLY • link 6.2 years ago Raymond ▴ 20