Question: Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
0
gravatar for Manik Garg
11 days ago by
Manik Garg0
Cambridge, UK
Manik Garg0 wrote:

Hi,

While running DESeq2, I corrected for covariates in the design formula and extracted the vst matrix with blind = FALSE. If I understand it correctly from here (https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#blind-dispersion-estimation), blind = FALSE takes into account the design formula so is my resulting vst matrix already corrected for covariates? I am asking this because I want to do downstream analysis such as running single sample GSEA (ssGSEA) and was wondering if using this vst matrix as input will already take into account the covariates and I might not have to correct for them later. Please let me know!

Thanks, Manik

deseq2 vst covariates • 48 views
ADD COMMENTlink modified 11 days ago by Michael Love24k • written 11 days ago by Manik Garg0
Answer: Is the data after variance stabilising transformation (blind = FALSE) already co
2
gravatar for Michael Love
11 days ago by
Michael Love24k
United States
Michael Love24k wrote:

No the transformations do not correct for the design. See the FAQ in the vignette for more detail (also brought up in recent posts here).

ADD COMMENTlink written 11 days ago by Michael Love24k

Thanks for your quick reply!

ADD REPLYlink written 11 days ago by Manik Garg0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 247 users visited in the last hour