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Messages - Wang

1
Vendor specific software / Re: Problems while using Compound Discoverer 3.2
Hi,

(1) I did some intensive tests on CD. The standard CD metabolomics workflow works pretty fine regarding RT alignment. Try to set high noise value. For instance, with our QE plus, we use 10e6 as noise threshold.

(2) If most of your peaks are not aligned, some unaligned peaks from different samples will of course be identified repeatedly. But also pay attention to structural isomers.

(3) Same could happen if most peaks are not aligned.

Wang




2
Other / Running msconvert with R?
Hi all,

I am trying to run MSConvert with R, but I got 127 error. What could be the problem?

Code: [Select]
msconvert <- "C:/Program Files (x86)/ProteoWizard/ProteoWizard 3.0.21175.5b6d9afee/msconvert.exe"
file <- "C:/Users/Desktop/Data/QC1.raw"
outfile <- "C:/Users/Desktop/Data"
convert <- paste0(msconvert," --mzXML, -o outfile -v", file)
system(convert)

Thanks for your help.


4
CAMERA / Feature selection for downstream statistics
Hi CAMERA users,

I want to perform statistics using the features generated by CAMERA, but I don't want to use all of them because many features represent the same "metabolite".

As features with the same PC label are supposed to belong to the same spectrum, can I just use features with a pattern of absence and a monoisotopic annotation for statistics?

Or do you have some other suggestions?

Thanks a lot.

Wang