This vignette gives an overview about importing files for downstream analysis with mpwR.
Importing the output files from each software can be easily performed with
prepare_mpwR. Please put all output files in one folder and follow the guidelines for naming the files. No other files/subfolders are allowed.
<- prepare_mpwR(path = "Path_to_Folder_with_files")files
The software output files need to be named according some simple rules.
Please use the following suffixes for the corresponding software:
Note that the suffixes for MaxQuant and ProteomeDiscoverer can be used as is.
Please use the same prefix for your analysis and the respective software output file(s). Each analysis needs a unique identifier.
Solution: Check your suffixes and make sure to use the correct spelling and the correct one for the respective software.
Solution: Make sure to include all output files from the respective software. MaxQuant requires 3 files, PD 4 files, DIA-NN and Spectronaut 1 file, respectively. Also use the same name (prefix) for all files.
Solution: Do not use subfolders in the directory of the output files. Put all files in a folder and use this path for prepare_mpwR.
Solution: Please use a unique name (prefix) for each respective output file(s). E.g. if you used…:
… the error message is displayed. As a solution, for example add the used software to the name:
Error in prepare_input(ordered_files[[i]][[“data”]][[“DIA-NN”]], software = “DIA-NN”) : Not all required columns present in submitted data.
Here example for DIA-NN. Similar messages for other software tools. Please make sure to include all required columns for the used software. Details are in the vignette Requirements.