Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
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Manik Garg • 0
@manik-garg-20656
Last seen 22 months ago
Cambridge, UK

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 • 262 views
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@mikelove
Last seen 1 day ago
United States

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).

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Thanks for your quick reply!

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