[BioC] justMAS and mas5

Crispin Miller CMiller at PICR.man.ac.uk
Mon Jun 27 12:45:29 CEST 2005

I've just had a look at this... I think you probably want a comma after
"1007_s_at"; exprs is a 2D matrix:

                 Note the comma

(exprs(j) should give you the same things as j at exprs)

I get the same results when I call justMAS more than once (trying to
duplicate your example).

If you're still having problems let me know - but with more details
(what version of R, what version of simpleaffy, what machine you're
running it on etc...). Hope that helps,


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Eitan
Sent: 24 June 2005 22:41
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] justMAS and mas5

   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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