Hi all,

I'm a little confused by Exon Array analysis in oligo. Specifically, I've been wondering if I should be correcting for GC content. The plots I get from following the vignette indicate that there is significant GC bias in my data, but the vignette doesn't appear to perform a GC correction later.

However, in investigating this, I've encountered another problem: I don't understand why I get two different answers when counting the number of perfect match features associated with the "core" meta-probeset (mps). Here's an example of what I'm doing, applied to the example data; any help would be greatly appreciated:


library(oligo)
library(pd.huex.1.0.st.v2)

library(oligoData)
data(affyExonFS)

nrow(exprs(affyExonFS))
## == 6553600 total features

length(pmSequence(affyExonFS, target="core"))
## == 893078 core-associated features


##get the feature sets associated with core mps
library(AnnotationDbi)
conn <- db(affyExonFS)
sql <- "SELECT fsetid from core_mps"
fsets <- dbGetQuery(conn, sql)$fsetid


sql <- "SELECT fsetid from pmfeature"
pmseq <- dbGetQuery(conn, sql)$fsetid

sum(pmseq %in% fsets)
## == 891084 core-associated features?

---------------

Thanks,

Jonathan


> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] AnnotationDbi_1.20.7    oligoData_1.8.0         pd.huex.1.0.st.v2_3.8.0
[4] RSQLite_0.11.2          DBI_0.2-5               oligo_1.22.0
[7] Biobase_2.18.0          oligoClasses_1.20.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         BiocInstaller_1.8.3
 [4] Biostrings_2.26.3     bit_1.1-10            codetools_0.2-8
 [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7
[10] IRanges_1.16.6        iterators_1.0.6       parallel_2.15.3
[13] preprocessCore_1.20.0 splines_2.15.3        stats4_2.15.3
[16] tools_2.15.3          zlibbioc_1.4.0


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