Question: DESeq2_variance stabilisation (rlog/vst) on cross species samples
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gravatar for adi.saxena
9 weeks ago by
adi.saxena0
adi.saxena0 wrote:

Hi

I want to perform DESEq2 vst and rlog variance stabilising transformations on gene counts from two different tissue types in two different mammalian species. I have two questions:

  1. Is there a disadvantage to performing vst/rlog only on a subset of genes that are significantly different in my DESeq2 DE analysis? or should I be doing these transformations on the entire GeneCount matrices?

  2. Does it matter if I perform these transformations using a matrix that has -

a. ALL genecounts from both tissue types in both species or

b. has counts for both tissue types in A species or

c. has genecounts from A tissue type in both species?

shall be grateful for any advice!

Thanks in advance, Adi

deseq2 • 97 views
ADD COMMENTlink modified 9 weeks ago by Michael Love24k • written 9 weeks ago by adi.saxena0
Answer: DESeq2_variance stabilisation (rlog/vst) on cross species samples
0
gravatar for Michael Love
9 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

VST and rlog need to learn the global trend of dispersion over mean. I recommend to use vst() and to run on the entire dataset (all genes, all samples).

ADD COMMENTlink written 9 weeks ago by Michael Love24k

Thanks for your help and advice!

ADD REPLYlink written 9 weeks ago by adi.saxena0
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