basismarkermap scaling fails for large data
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thrabe • 0
@thrabe-9205
Last seen 5.9 years ago
United States

Hi there, I have trouble with the basismarkermap plot. The ExpressionMix I use is contains 115 samples, and when I plot it with HaemAtlas markers mapped onto Affymatrix IDs the final plot is extremely detoriated, the matrix is half truncated at the right edge for instance. The cause for this behavior is the unproportional scalling between the marker dots on the left and the matrix. The marker dot plot area grows with the datasize while the matrix shirks. However, this should be opposite - matrix grows and dot area shrinks? This starts at a datasize beyond 30 samples.  It's the same behaviour in RStudio and R in the terminal. I could share data on request.

Here's my code

load(anExpressionSetFile)
  
  markerList <- MarkerList('HaemAtlas')
  
  eMix = ExpressionMix(eset[,startSample:endSample])
  
  #converts Illumina IDs to hthgu133pluspm IDs 
  convertedIDs <- convertIDs(markerList, eMix, method='1:1', verbose=FALSE)
basismarkermap(convertedIDs[,1:10],eMix)

 

 

Cellmix • 687 views
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