[BioC] Why mm's changing after bg.adjust.gcrma?

[Jenny Drnevich]

Hello,

I just noticed an odd behavior of bg.adjust.gcrma - I thought it was only 
supposed to change the pm values, not mm values, according to the help 
page: "The returned value is an 'AffyBatch' object, in which the PM probe
      intensities have been background adjusted. The rest is left the
      same as the starting 'AffyBatch' object."

However, my mm values are changing (example code below) for all genes 
except those starting with "AFFX" on Affy's soybean chip. I also checked 
this behavior for some drosgenome1 chips, and there all the mm values are 
changing, even for "AFFX" genes. The changing mm values aren't causing me 
any problems, but I thought that since they weren't supposed to change I 
would ask about it. I came across this issue trying to figure out why my 
adjusted pm values change when I remove some probesets before doing 
bg.adjust.gcrma, but that's another posting...

Thanks,
Jenny


 > gc.abatch <- bg.adjust.gcrma(raw.data)

#The first 135 genes start with "AFFX"
 > sum( mm( raw.data, allgenenames[1:135]) - 
mm(gc.abatch,allgenenames[1:135]) ==0)
[1] 10680

 > length( mm( raw.data, allgenenames[1:135]) - 
mm(gc.abatch,allgenenames[1:135]))
[1] 10680

 > sum( mm( raw.data, allgenenames[136:270]) - mm( gc.abatch, 
allgenenames[136:270]) ==0)
[1] 0

 > sessionInfo()
Version 2.3.0 (2006-04-24)
i386-pc-mingw32

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
drosgenome1cdf   soybeanprobe     soybeancdf          made4  scatterplot3d
       "1.12.0"       "1.12.0"       "1.12.0"        "1.6.0"       "0.3-24"
           ade4   affyQCReport     simpleaffy     genefilter       survival
        "1.4-1"       "1.10.0"        "2.6.0"       "1.10.1"         "2.24"
     reposTools        affyPLM          gcrma    matchprobes       affydata
       "1.10.0"        "1.8.0"        "2.4.1"        "1.4.0"        "1.8.0"
           affy         affyio        Biobase          limma        RWinEdt
       "1.10.0"        "1.0.0"       "1.10.0"        "2.7.2"        "1.7-4"
 >



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu