I had a question in regards to the "S2_Protein_Limma.R" script. In my experiment I do not have the TMT experiments, it is just a DDA (LFQ) run for phosphoproteomics in which I have the intensity for each individual run. When I run the script it tell me below the "Error: Problem with filter() input ..1.
i Input ..1 is Intensity > 0.
x object 'Intensity' not found"
I already changed my "Sample_metadata.tsv" based on my experiment and the name of the samples, however I am not sure which name in this file should match which columns in "ptoteingroup.txt or Phospho (STY)Sites.txt
I am sending my files, I would appreciate if someone can please let me know if the names are set correctly, or how should I fix this error to proceed with the analysis.
Hello,
I had a question in regards to the "S2_Protein_Limma.R" script. In my experiment I do not have the TMT experiments, it is just a DDA (LFQ) run for phosphoproteomics in which I have the intensity for each individual run. When I run the script it tell me below the "Error: Problem with
filter()input..1. i Input..1isIntensity > 0. x object 'Intensity' not found"I already changed my "Sample_metadata.tsv" based on my experiment and the name of the samples, however I am not sure which name in this file should match which columns in "ptoteingroup.txt or Phospho (STY)Sites.txt I am sending my files, I would appreciate if someone can please let me know if the names are set correctly, or how should I fix this error to proceed with the analysis.
Thank you so much. Sample_metadata.txt proteinGroups.txt Phospho (STY)Sites.txt