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Question: Package won't recognise raw data files
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gravatar for bhgyu
8 days ago by
bhgyu20
bhgyu20 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 8 days ago by bhgyu20

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 8 days ago by Johannes Rainer1.1k
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