[BioC] help with multtest and annaffy

[Taylor, Katie]

Hi,

I have followed the annaffy vignette online and successfully created the HTML documents for annotating the aafExpr dataset. When I try to do the same with my data (GDS2609) which I downloaded from GEO I can only get so far and then R becomes unresponsive and is forced to close. I have copied the session info below:

'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affy); library(limma)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> Data <- ReadAffy()
> Gds2609 <- Data
> eset <- rma(Gds2609)
Background correcting
Normalizing
Calculating Expression
> pData(eset)
             sample
GSM93789.CEL      1
GSM93920.CEL      2
GSM93952.CEL      3
GSM93954.CEL      4
> strain <- c("n", "n", "c", "c")
> design <- model.matrix(~factor(strain))
> colnames(design) <- c("n", "c")
> design
  n c
1 1 1
2 1 1
3 1 0
4 1 0
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$`factor(strain)`
[1] "contr.treatment"
 library(multtest)
> class <- as.integer(pData(Gds2609)$covar1) - 1
>  teststat <- mt.teststat(exprs(Gds2609), class) ##at this point R is forced to close each time I try it. 
> sessionInfo() ## had to do this command before teststat otherwise R closes before I can do it
R version 2.11.0 (2010-04-22) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] multtest_2.4.0       hgu133plus2cdf_2.6.0 limma_3.4.0         
[4] affy_1.26.0          Biobase_2.8.0       

loaded via a namespace (and not attached):
[1] affyio_1.16.0         MASS_7.3-5            preprocessCore_1.10.0
[4] splines_2.11.0        survival_2.35-8       tools_2.11.0         
> 


The commands that I want to use after this are as follows:
index <- order(abs(teststat), decreasing = TRUE)
probeids <- featureNames(Gds2609)[index]
library(annaffy)
aaf.handler()
anncols <- aaf.handler()[c(1:3, 8:9, 11:13)]
anntable <- aafTableAnn(probeids[1:250], "hgu133plus2.db", anncols)
saveHTML(anntable, "example1.html", title = "Example Table without Data")
testtable <- aafTable(`t-statistic` = teststat[index[1:250]],
signed = TRUE)
table <- merge(anntable, testtable)
exprtable <- aafTableInt(Gds2609, probeids = probeids[1:250])
table <- merge(table, exprtable)
saveHTML(table, "example2.html", title = "Example Table with Data")
saveText(table, "example2.txt")


If anyone has any ideas why R keeps closing on me like this I would really appreciate your help. I've tried running R on different computers as I didn't know if it was a memory problem but the example in the annaffy pdf works fine. I have no idea what is happening and could really do with some help.

Best Wishes,

Katie