Bithorax

icon company Centre for molecular informatics, University of Cambridge icon location Cambridge, United Kingdom icon location Working as Computational Toxicologist in the area of using gene expression data for risk assessment.

Results 4 comments of Bithorax

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

Hi, I'm currently doing something similar to you. To answer your question I would say that batch correction should be the first step as it requires raw data as input....

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

One last question if you can help. I'm not quite sure when I should specify the "group" and hence "full mod=TRUE" parameters. do you have an explanation?

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

Thanks for the explanation. Just a doubt. If specifying "batch" is only removing the batch effect from the dataset, then automatically the signal of my variables of interest are kept....

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

Yes, I see your point and I agree. It would be curious to compare the two models to see the difference in the signal. But I guess this also depends...