[BioC] results.summary function returns error

[Steve Lianoglou]

Hi Julia,

You are using a rather outdated version of R and Bioconductor at this point.

I'd suggest you upgrade to the latest version of R (2.15.2) and
reinstall the relevant bioconductor packages via:

R> source("http://bioconductor.org/biocLite.R")
R> biocLite(c('your', 'packages', 'of', 'interest'))

I'm not too familiar w/ the workings of the simpleaffy package, so
can't really comment on your code, per se, but you'll need current
versions of the packages you're using to get the best help (these
problems might even disappear on their own).

-steve

On Fri, Nov 16, 2012 at 4:49 AM, Julia Jacobson [guest]
<guest at bioconductor.org> wrote:
>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact