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Topic: Blank subtraction (Read 409 times) previous topic - next topic

  • polbeik
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Blank subtraction

I am wondering whether I can subtract a blank from a sample, before I process it with xcms, or at least right after I convert it to an xcmsSet object. The procedure I follow for now is the following:
I have 1 blank and 2 samples. I copy the blank .mzXML and paste it to make it like a second blank .mzXML  (fake blank). I create 2 files "blank" and "samples", with 2 .mzXML each and I use xcmsSet command. I get the diffreport excel file and then I subtract the rows of the diffreport that have negative tstatistic (which means that the blank's signal is higher than the sample's) and also all raws, that have non zero number of peaks for the blank. This way I get the final diffreport, which I hope that it corresponds only to reliable peaks, but I am not sure. I also want to use xsAnnotate command (CAMERA package), but I am not sure if I can, because this command must be applied to the xcmsSet object, which it contains many peaks that correspond to the blank and not to the sample. 

Thank you!!