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statOmics / msqrob2

Implementation of the MSqRob analysis of differentially expressed proteins using the Features infrastructure
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Dependecy issues #10

Closed ococrook closed 4 years ago

ococrook commented 4 years ago

Hi Lievent,

I'm just working through some of the .rmd flles. I'm not sure which version of Features you are using but I'm a little confused in the cptac.Rmd

for example in line 81, I think it should be logAssay rather than peptide:

pe <- logTransform(pe, base = 2, i = 1)
limma::plotDensities(assay(pe[["logAssay"]]))

If that's correct then I can push I bunch on changes but then I can get an error at:

pe <- msqrob(object = pe, i = "protein", formula = ~condition)

Error in df.residual < 2L : comparison (3) is possible only for atomic and list types.

I think this happen because of problems with aggregateFeature, but I think you know what's going on with the code better than me. I can push a few changes, but could you confirm?

statOmics commented 4 years ago

Bug with respect to df.residual is solved. cptac script is now compliant with most recent version of Features