[BioC] results.summary function returns error

[James W. MacDonald]

Hi Julia,

On 11/16/2012 4:49 AM, Julia Jacobson [guest] 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")

But this isn't the same thing as what is in the vignette:

summary <- results.summary(pw.filtered,"hgu133a")

Note that there isn't a .db extension.

> Error is get(paste(cdfname, "SYMBOL", sep = "")) :
>    Object "hgu133a.dbSymbol" not found

Hence the error. Even though the annotation packages now use a SQLite 
backend, the 'regular' get() and mget() functions still work. But the 
environment argument is still hgu133aSYMBOL, not the hgu133a.dbSYMBOL 
that ends up being used in your case.

Best,

Jim


>
> 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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099