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Topic: Problem with file uploading to metaXCMS (Read 4700 times) previous topic - next topic

Problem with file uploading to metaXCMS

how to trace the previously saved file on metaXCMS.
I uploaded files to metaXCMS,but It coudn't proceed further because of previously saved file and I got an error message "Error in if (xcmsFiles.df[f, "ControlIs"] == xcmsFiles.df[f, "Class2"]) upid <- !upid :
  missing value where TRUE/FALSE needed.

I deleted .Rdata and .Rhistory files and searched in all drives and on desktop for saved file. but still I could not trace out the file which was saved in metaXCMS.
please find attached here with file.

Re: Problem with file uploading to metaXCMS

Reply #1
The XCMS Online result has many additional columns compared to XCMS output.
That also means that these results are not compatible with the current metaXCMS version.
The only workaround at the moment is to process the data using XCMS as described in the protocol.

Re: Problem with file uploading to metaXCMS

Reply #2
I am using XCMS online because it has more parameters and advanced than XCMS.so can I try with XCMS online data by deleting extra columns(ex:f value,qvalue...etc)

Re: Problem with file uploading to metaXCMS

Reply #3
Hi Ralf,
even I have the same problem with this saved file in metaXCMS,but I use to do xcms online data processing with metaXCMS(I dint face any compatibility problem),but when I face this saved file problem, I just remove R and reinstall everything.

Re: Problem with file uploading to metaXCMS

Reply #4
Without a guaranty that it works:

You can make it somewhat compatible if you
- make sure the retention time format is seconds
- delete the additional columns

If you want to use metaXCMS' retention time correction and EIC function than it also needs the raw data.
Then the dataset names in the table have to match the folder names with the raw data. These folders that contain the raw data have to be in the same folder as your csv/tsv/xlsx file.