[BioC] memory invalid permission with qc()

[Wolfgang Huber]

Simon Noël ha scritto:
> Hello.  I have some problem using qc().  I have an old data set that work
> perfectly with qc() but a nuw one just arrive from affymetrix and I am not able
> to run qc() on it.  I use the code :
> 
> library(affy)
> 
> 
> 
> library(affyio)
> 
> 
> library(simpleaffy)
> 
> Data <-ReadAffy()
> 
> qc <- qc(Data)
> 
> and I recive this error message :
> 
> *** caught segfault ***
> address 0xb6cf9000, cause 'invalid permissions'
> 
> Traceback:
>  1: .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[,     x]),
> as.character(pns), as.integer(length(mms[, x])), as.double(ct),    
> as.double(st), exprs = double(length(unique.pns)), length(unique.pns),    
> PACKAGE = "simpleaffy")
>  2: FUN(1:2[[1L]], ...)
>  3: lapply(X, FUN, ...)
>  4: sapply(1:length(pms[1, ]), function(x) {    .C("GetExpressionLevels",
> as.double(pms[, x]), as.double(mms[,         x]), as.character(pns),
> as.integer(length(mms[, x])),         as.double(ct), as.double(st), exprs =
> double(length(unique.pns)),         length(unique.pns), PACKAGE =
> "simpleaffy")$exprs})
>  5: justMAS(x, tgt = sc)
>  6: call.exprs(unnormalised, "mas5")
>  7: qc.affy(unnormalised, ...)
>  8: qc(Data)
>  9: qc(Data)
> 10: eval.with.vis(expr, envir, enclos)
> 11: eval.with.vis(ei, envir)
> 12: source("tmp.R")
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> 
> What should I do to correct the problem?
> 
> Simon Noël
> VP Externe CADEUL
> Association des étudiants et étudiantes en Biochimie, Bio-
> informatique et Microbiologie de l'Université Laval
> CdeC



Dear Simon

what is your "sessionInfo()"?

Are you using the latest release of R (2.9) and Bioconductor?

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber