SARTools and batch effects

Question

[skhan]

According to the SARTools vignette (https://github.com/PF2-pasteur-fr/SARTools/blob/master/vignettes/SARTools.rmd), we can, in the 4th column of the target file, supply further information about the samples to correct for batch effects.

Can we correct for multiple different batch effects, perhaps by having a 5th, 6th, and 7th column? As an example, I would want to correct for gender, age, tissue, and dissection date.

[Thibault D.]

Hi, as far as I read the doc, I think you can provide multiple columns and use a R-formula to give a more complex design to SARTools. Remember, it depends on the tool you're using within SARTools (DESeq2 or EdgeR). You may have to refer to their own documentations.