Differential analysis of protein spectral counts using msnSet object
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@javan-okendo-22941
Last seen 5 months ago
University of Cape Town

I have an MsnSet object which I would like to use for the differential analysis of the proteomics data using spectral counts information. Below is the MsnSet object and I am wondering how to add the "phenoData" in this object. Kindly help

> msnset
MSnSet (storageMode: lockedEnvironment)
assayData: 1535 features, 27 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData
  featureNames: sp|A0A075B6H7|KV37_HUMAN sp|A0A075B6H9|LV469_HUMAN ...
    tr|V9GZ38|V9GZ38_HUMAN (1535 total)
  fvarLabels: peptide accession
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
- - - Processing information - - -
Subset [16227,27][6518,27] Tue Jun  9 22:14:01 2020 
Combined 6518 features into 1535 using sum: Tue Jun  9 22:14:02 2020 
 MSnbase version: 2.10.1 `
annotation edger • 197 views
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I removed the DESeq2 tag from this post, as this is out of scope for support at least.

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@kevin
Last seen 29 minutes ago
Republic of Ireland

You should be able to assign pData via, for example:

pData(msnset) <- pd

Kevin

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