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Hello everybody out there using the simpleaffy Bioconductor package,
In order to get started with microarray analysis, I'm trying to
reproduce the steps in the Vignette of the simpleaffy package.
I downloaded the sample CEL files from the homepage of the
bioinformatics group of the university of Manchester
(http://bioinformatics.picr.man.ac.uk/experiments/amplification/CEL/)
and performed the following steps:
R> library(simpleaffy)
R> x <- read.affy("covdesc")
R> x.rma <- call.exprs(x,"rma")
R> pw <- pairwise.comparison(x.rma,"rna",c("10ng","100ng"))
R> pw.filtered <- pairwise.filter(pw)
R> library("hgu133a.db")
So far, so good. The following command yields the error message:
R> summary <- results.summary(pw.filtered,"hgu133a.db")
Error is get(paste(cdfname, "SYMBOL", sep = "")) :
Object "hgu133a.dbSymbol" not found
I've done extensive web search and found out there's been a migration
of the annotation data to SQLite format. This seems to cause problems
concerning the annotation carried out by the "results.summary"
function.
In the thread
https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html
is mentioning a very similar problem I have and solves this thread by
redefining the "get.annotation" function
get.annotation <- function (x, cdfname, verbose = FALSE) {
library(cdfname, character.only = TRUE)
cdfname <- sub("\\.db$", "", cdfname) ## add this line
}
I tried this to no success.
Moreover, I entered the following commands, but also got errors:
R> summary <- results.summary(pw.filtered,hgu133a.db)
R> summary <- results.summary(pw.filtered,"hgu133a")
R> summary <- results.summary(pw.filtered,hgu133a)
What additional diagnostics could I run to pin down the problem?
Kind regards,
Julia
-- output of sessionInfo():
R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu133a.db_2.6.3 org.Hs.eg.db_2.6.4 RSQLite_0.11.2
[4] DBI_0.2-5 hgu133acdf_2.9.1 AnnotationDbi_1.16.19
[7] simpleaffy_2.30.0 gcrma_2.26.0 genefilter_1.36.0
[10] affy_1.32.1 Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affyio_1.22.0 annotate_1.32.3 BiocInstaller_1.2.1
[4] Biostrings_2.22.0 IRanges_1.12.6 preprocessCore_1.16.0
[7] splines_2.14.1 survival_2.36-10 tools_2.14.1
[10] xtable_1.7-0 zlibbioc_1.0.1
--
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