[BioC] justMAS and mas5

[Eitan Halper-Stromberg]

Hi,
   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   
6.036457

 > 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   
7.311159

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.

-Eitan