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mildpiggy / DEP2

An r package for proteomics data Analysis, developed from DEP.
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```impute()``` with zero values #7

Closed cathalgking closed 6 months ago

cathalgking commented 7 months ago

I would like to just replace any missing values with 0 when using the impute() function. Can this be done with the below code? The function reference page does not specify this.

imputed_MLE <- impute(norm, fun = "zero")
mildpiggy commented 7 months ago

Yes. You can specify the DEP2::impute to avoid the confusion of functions with the same name (could from other packages).

imputed_zero <- DEP2::impute(norm, fun = "zero")
cathalgking commented 6 months ago

Hi @mildpiggy That makes sense thanks. Just to confirm, DEP2 cannot correct for batch effects in proteomics data? I have 6 plates that I would like to correct for technical effects if any. Can you recommend a package that can do this?

mildpiggy commented 6 months ago

@cathalgking DEP2 cannot correct the batch effects cross experiments. You can try other tools for this job. Maybe you can begin from statTarget as i said https://github.com/mildpiggy/DEP2/issues/4#issuecomment-2063578307. However, as far as I can remember, this tool requires an old version of R.