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Question: Package won't recognise raw data files
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gravatar for bhgyu
13 months ago by
bhgyu30
bhgyu30 wrote:

Hi guys, 

I'm running the CAMERA package from bioconductor. 

I've created an xcmsSet by c-binding multiple single xcmsSets, which all works fine. However, when I then later come back to the saved session to do annotation, Camera throws in the following error:

xsaC <- groupCorr(xsaF) 
Start grouping after correlation.
Generating EIC's .. 
Error in getAllPeakEICs(object, index = index) : 
  Raw data file:D:/Metab/Data/DATA FOR R/Aqueous Neg/SJ55.CDF not found ! 

I've set the working directory to 

D:/Metab/Data/DATA FOR R/Aqueous Neg which contains all the raw files including SJ55.CDF, but the error remains. 

Can I somehow point to the file for the package to recognise it?


Cheers!

 

ADD COMMENTlink written 13 months ago by bhgyu30

Did you move the original CDF files after having performed the peak detection?

what is the output of filepaths(xsaF) (assuming xsaF is an xcmsSet object)?

And can you please provide the output from sessionInfo()?

ADD REPLYlink written 13 months ago by Johannes Rainer1.3k
1

Yes, they were moved between computers,

Overwriting "filepaths" works!

ADD REPLYlink modified 12 months ago • written 12 months ago by bhgyu30
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