dataProcess issue

[Eren Boybay]

Error: Elements listed in `by` must be valid column names in x and y In addition: Warning message: Input data.table 'y' has no columns. 

Currently having this issue when trying to perform dataprocess on my Skyline data report and have run out of potential ideas on what this issue relates to ?

[Anthony Wu]

Hi,

Did you run the "SkylinetoMSstatsFormat" converter before running the "dataProcess" function?  Seems similar to this issue where the user didn't run the MSstats converter beforehand.

If running the "SkylinetoMSstatsFormat" converter doesn't work, could you send me your dataset and I can debug on my side?

Thanks,

Tony

[Anthony Wu]

Update on this thread:

For those who may encounter this, you may have rows where the FragmentIon column contains "precursor", "precursor [M+1]", etc, but for DIA/SRM datasets, those rows need to be removed for MSstats since MSstats performs differential abundance analysis at the fragment ion level (and not precursor level).  

When exporting MSstats from Skyline, you can hit preview and filter out rows containing "precursor".  See screenshots.

Tony