We have had some HuProt (protein microarrays) arrays done as well as some preliminary analysis done, giving fold changes and p-values for s simple case-control cohort.
We would like to do some more detailed analysis based on further clinical data (such as stratify cases into acute and chronic vs control). I am familiar with R, and have analysed RNAseq data with it before from count tables, using DESeq2, but know this would not be appropriate for the protein array analysis.
With DEseq I can Strat with a "counts table" and "metadata" table and carry out any of the analysis I would like.
I am however not familiar with protein array data and would like to know which format of data I should ask for from the company that is similar to the normalised "counts" data from RNA seq. Essentially protein abundance per patient. And additionally what R package can I use to analyse this protein a abundance data from this point?