[BioC] Why mm's changing after bg.adjust.gcrma?
Jenny Drnevich
drnevich at uiuc.edu
Thu May 25 21:22:28 CEST 2006
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
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