Exon Arrays - GC & how many pm features?
0
0
Entering edit mode
@jonathan-cairns-5761
Last seen 7.0 years ago
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 [[alternative HTML version deleted]]
oligo oligo • 565 views
ADD COMMENT

Login before adding your answer.

Traffic: 262 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6