mitch analysis on R

Question

[Amr]

In mitch analysis on R while importing the profiling data

x <- list("dge1"=dge1, "dge2"=dge2)

y <- mitch_import(x, DEtype="edger")

What is dge1 and dge2, what data should i write or put here? also DEtype is 'edger' is it always edger or changed as DESeq if I performed DESeq2 to normalize the data?

reference: https://github.com/markziemann/mitch

Thanks

[andres.firrincieli]

What is dge1 and dge2, what data should i write or put here? also DEtype is 'edger' is it always edger or changed as DESeq if I performed DESeq2 to normalize the data?

You should check the RData files in the data folder to understand what kind of data mitch requires. By looking at the description mitch can take as input the result tables (dge) generated by different DGE analysis software.

ps. you can't use mitch with just two conditions where only one contrast is possible: Mutated vs Normal

[Amr]

Thanks now dge is clear, so dge is the results table after dds, what about DEtype? If I used DESeq, then should I change "edger" to "DESeq2" or what ?

[andres.firrincieli]

f I used DESeq, then should I change "edger" to "DESeq2" or what ?

In general, if you have any doubt about how a function works always check the usage first, and then ask the question. See mitch_import usage