[BioC] filtering Gene 1.0 ST chips

Dennis Burian dburian at cox.net
Fri Feb 15 22:16:27 CET 2013


I have a large time course experiment on Gene 1.0 ST GeneChips that I'm
analyzing with the oligo and timecourse packages in Bioconductor. In my
experimental design, this analysis method determines genes most likely
to have different temporal expression patterns between two biological
conditions.

Where I'm running into trouble is many of my highest scoring genes are
intronic and exonic controls. I surmise that the software is scoring
these probe sets highly because they are "expressed" at very low but
noisy levels. Examination of the expression profiles confirms this
hypothesis, expression levels between 0 and 4 so I'm not concerned about
quality of the data.

>From the oligo.pdf manual in rma-methods, core is the default setting
for target. My question is whether there is another setting for target
that would filter out the intronic/exonic control probe sets prior to
differential expression testing? Is subset implemented and if so what
flag would I use to take advantage of it?

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=C                LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] pd.hugene.1.0.st.v1_3.6.0 RSQLite_0.11.2           
[3] DBI_0.2-5                 timecourse_1.28.0        
[5] MASS_7.3-22               oligo_1.20.4             
[7] oligoClasses_1.18.0      

loaded via a namespace (and not attached):
 [1] affxparser_1.28.1     affyio_1.24.0         Biobase_2.16.0       
 [4] BiocGenerics_0.2.0    BiocInstaller_1.4.9   Biostrings_2.24.1    
 [7] bit_1.1-9             codetools_0.2-8       compiler_2.15.0      
[10] ff_2.2-10             foreach_1.4.0         IRanges_1.14.4       
[13] iterators_1.0.6       limma_3.12.3          marray_1.34.0        
[16] preprocessCore_1.18.0 splines_2.15.0        stats4_2.15.0        
[19] tools_2.15.0          zlibbioc_1.2.0       
> 

Many thanks,
Dennis Burian



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