I am trying to remove the batch effect from my RNSeq Data. I hope someone can help me determine how my correction has gone, has it worked.
Using Combat: I used combat to correct for batch. The resulting MSDplot gives signficantly better grouping of the sampels on the basis of condition. However, the comat requires log transformed data, so I need to revese transform the data to use in DESeq. I can do that, but after doing that and doing differential analysis, is there a way I can compare my combat-corrected data with the un-corrected data ? (Just wondering because I need to reverse log transform)?
I can use svaseq, which gives me surrogate variations to model the RNASeq data.
ddssva <- dds ddssva$SV1 <- svseq$sv[,1] ddssva$SV2 <- svseq$sv[,2] design(ddssva) <- ~ SV1 + SV2 + condition
how to visualise the correction.
i tried following this. http://genomicsclass.github.io/book/pages/adjusting_with_factor_analysis.html