When I want to align my data or produce EICs with metaXCMS, nothing is happening. In R an error message appears:
Error in xcms:::phenoDataFromPaths(files) : Directory tree must be level
What can I do about this?
How many XCMS results are you trying to compare ?
Did you move the raw data out of/within the XCMS result folder ?
I am trying to compare 5 XCMS results.
I moved the raw data within the XCMS result folder.
Since metaXCMS needs to see the raw data in exactly the same way (,i.e. folder, name) XCMS processed it
it does not work if you move the raw data after XCMS processing.
Hi
I have exactly the same problem. I am trying to compare three XCMS results and I have not moved or renamed any folders or data. This problem causes my PC to freeze when I run alignment of data or try to produce EICs in metaXCMS. When I reload R and try again, there is already data loaded onto metaXCMS which stops me from going any further with a new analysis.
Please help!
Please make sure that R does not save the workspace.
If the workspace has already been saved, locate and delete it (.RData file).
Re-alignment and creating the EIC's does take a while, though ... it will reprocess all your raw data.
If you do not see the progress bar for some reason, the R console should show what R is currently doing (or not doing if there is an error).
I can also add that I was able to get rid of this error by starting all my analyses from one common upper level folder. My first attempt at leaving all the XCMS files in place, but having them in different directories also resulted in the error about directory level not being flat.