[BioC] NUSE and RLE PLOTS for ST1.0 Gene chips with oligo w/o 1st quantile line

[Richard Friedman]

Dear Bioconductor List,

	I am processing Affymetrix Mouse ST1.0 Gene chips with oligo.
The first quantile line doesn't seem to be visible on the NUSE and RLE  
plots.
In my past experience with NUSE and RLE plots for Mous2 430.2 chips,
the second quantile line was visible. Here it is not. I am wondering if
this is a property of ST1.0 chips in general, a bug in the NUSE  
program for
this class of chips, or is indicative of a problem with this dataset.
This last option is especially important, as I have not observed  
statistically significant differential
expression with this dataset. I would greatly appreciate it if someone  
more experienced with
ST1.0 Gene chips and oligo than myself could at the plots. If anyone  
can look at them I will send them
offline.

My script is:

plm<-fitPLM(raw)

png("NUSE.png")
boxplot(plm,ylim=c(0.9,1.1),main="NUSE")
dev.off()

png("NUSEfull.png")
boxplot(plm,main="NUSE")
dev.off()


png("RLE.png")
boxplot(plm,ylim=c(0.9,1.1),main="RLE")
dev.off()

png("RLEfull.png")
boxplot(plm,main="RLE")
dev.off()

My session is (at I hope that using R2.13.0 is not a problem:

R version 2.13.0 (2011-04-13)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_3.8.1               pd.mogene.1.0.st.v1_3.2.0  
RSQLite_0.9-4             DBI_0.2-5
[5] oligo_1.16.2              preprocessCore_1.14.0      
oligoClasses_1.14.0       Biobase_2.12.1

loaded via a namespace (and not attached):
[1] affxparser_1.24.0 affyio_1.20.0     Biostrings_2.20.0  
bit_1.1-7         ff_2.2-3
[6] IRanges_1.10.0    splines_2.13.0

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

I am a Bayesian. When I see a multiple-choice question on a test and I  
don't
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14