[BioC] justMAS and mas5

Eitan Halper-Stromberg eitan.halper-stromberg at nist.gov
Fri Jun 24 23:40:54 CEST 2005

   I am trying to speed up my mas5 processing by using justMAS on my  
affybatch. My AffyBatch is made of 8 chips and the cdf for these  
chips is hgu133a. I have tested justMAS by running it several times  
on this affybatch and I am obtaining different expression measure  
results even though I am doing the exact same command. My affybatch  
is called 'F'  and an array of geneNames is called 'gn', and I type:

 > j<-justMAS(F)

 > j at exprs[gn=="1007_s_at"]
1007_s_at      <NA>      <NA>      <NA>      <NA>      <NA>       
<NA>      <NA>
6.603113  6.171309  6.399581  6.171309  6.171309  6.171309  6.171309   

 > i<-justMAS(F)

 > i at exprs[gn=="1007_s_at"]
1007_s_at      <NA>      <NA>      <NA>      <NA>      <NA>       
<NA>      <NA>
6.603113       NaN  6.171309  5.482231  6.171309  5.438713  5.387300   

Does anybody know why I am getting this discrepancy?

I am running the justMAS function from the simpleaffy library. On  
another note, it also appears that the mas5 function is giving me  
enigmatic results in the same fashion as just stated.


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