proteoQC throwing error after running
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laural710 • 0
Last seen 2.8 years ago

The proteoQC package is exactly what i was looking for to give me some QC information on proteomic samples, however i am running into two issues. One may be a bug, and the other may be me doing something weird.

The first is that when i am creating the sample list to run with the mQCpipe, it will only work if i have all the headings outlined in the example (file, sample, bioRep, techRep and fraction). I have many biological replicates (currently running 5 biological replicates per 2 samples to test the system but this will typically increase to 10-15 per sample) but i do not run technical replicates or have fractions. To get around this, i have been inserting either 1 or 0 and it has been running fine resulting in a mQC file. Is this a bug in the code, or do i need to specify something indicating that i do not have technical replicates or fractions? I have ran the example sample with this and then removing the fraction and tech and it also does not run which is why i wonder if it is a bug.

Secondly, when i use the reportHTML on my mQC file, the following error appears

Error in names(miss.df) <- c("x", "y") : 'names' attribute [2] must be the same length as the vector [1]

Looking into the names, there is an obvious difference where my run returns the following headings ("inputparameter" "resfractionlevel" "restechReplevel" "ressample_level") but does not include the biological replicate column despite this containing most of the sample information.

Any help with this would be much appreciated as i'm running out of ideas.

ProteoQC Proteomics • 306 views

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