[BioC] Bioconductor 1..6.1: espresso problem.

[Laurent Gautier]

On Tue, Jan 07, 2003 at 02:13:05PM -0500, Johanne Duhaime wrote:
> Hello
> 
> I am a new user of Bioconductor. I just installed version 1.1 on R
> version 1.6.1. This is done on widows 2000.
> I want to reproduce section 3.3 "Expression measures" of the document
> "Textual Description of affy". But I keep having the same error whatever
> I tried.
> Can you help me? Thank you in advance.
> 
> 
> > ReadAffy()
> AffyBatch object
> size of arrays=640x640 features (16003 kb)
> cdf=MG_U74A (12654 affyids)
> number of samples=5
> number of genes=12654
> annotation=mgu74a
> notes=
> > ls()
> character(0)
> > eset <-
> expresso(affybatch,normalize.method="qspline",bg.method="rma",summary.method="liwong")
> 
> Error in expresso(affybatch, normalize.method = "qspline", bg.method =
> "rma",  :
>         unused argument(s) (bg.method ...)
> 

Thanks for pointing it out. This part of the doc relates to the previous version of the package. One should read:
eset <- expresso(affybatch.example, normalize.method="loess", bgcorrect.method="rma", pmcorrect.method="pmonly", summary.method="liwong")

Unfortunately, it revealed an another problem (particular to few datasets, among which 'affybatch.example'). The fix should appear by tomorrow in th repository. You can copy paste the following in your session in the meanwhile:
(note 'qspline' is stil not very 'bugfree'... works for some sets, crashes on others... we are on the case...)



Hopin' it helps,



L.


# ---------------------
library(affy)
where <- as.environment("package:affy")
  setMethod("computeExprSet", signature(x="AffyBatch", pmcorrect.method="character", summary.method="character"),
            function(x, pmcorrect.method, summary.method, ids=NULL,
                     verbose=TRUE, summary.param=list(),
                     pmcorrect.param=list(), warnings=TRUE)
            {
              
              pmcorrect.method<- match.arg(pmcorrect.method, pmcorrect.methods)
              summary.method <- match.arg(summary.method, express.summary.stat.methods)
              
              n <- length(x)
              
              ## if NULL compute for all
              if (is.null(ids))
                ids <- geneNames(x)
              
              m <- length(ids)

              ## cheap trick to (try to) save time
              c.pps <- new("ProbeSet",
                           pm=matrix(),
                           mm=matrix())
              
              ## matrix to hold expression values
              exp.mat <- matrix(NA, m, n)
              se.mat <- matrix(NA, m, n)

              if (verbose) {
                cat(m, "ids to be processed\n")
                countprogress <- 0
              }
              
              ## loop over the ids
              mycall <- as.call(c(getMethod("express.summary.stat",
                                            signature=c("ProbeSet","character", "character")),
                                  list(c.pps, pmcorrect=pmcorrect.method, summary=summary.method,
                                       summary.param=summary.param, pmcorrect.param=pmcorrect.param))
                                )
              ##only one character cause no more bg correct
              ##bg.correct=bg.method, param.bg.correct=bg.param,
              
              ##WHy not show error? took it out cause sometimes we
              ##get errors and couldnt see them.
              ##options(show.error.messages = FALSE)
              ##on.exit(options(show.error.messages = TRUE))
              
              CDFINFO <- getCdfInfo(x) ##do it once!
              
              for (i in seq(along=ids)) {
                
                id <- ids[i]
                
                if (verbose) {
                  if ( round(m/10) == countprogress) {
                    cat(".")
                    countprogress <- 0
                  }
                  else
                    countprogress <- countprogress + 1
                }
                ## locations for an id
                ##l.pm <- locate.name(ids[id], cdf, type="pm")
                ##l.mm <- locate.name(ids[id], cdf, type="mm")
                loc <- get(id, envir=CDFINFO)
                l.pm <- loc[, 1]
                if (ncol(loc) == 2)
                  l.mm <- loc[ ,2]
                else
                  l.mm <- integer()
                
                np <- length(l.pm)
                
                ##names are skipped

                c.pps@pm <- intensity(x)[l.pm, , drop=FALSE]
                c.pps@mm <- intensity(x)[l.mm, , drop=FALSE]
                
                ## generate expression values
                ## (wrapped in a sort of try/catch)
                mycall[[2]] <- c.pps
                ev <- try(eval(mycall))
                
                if (! inherits(ev, "try-error")) {
                  exp.mat[i, ] <- ev$exprs
                  se.mat[i,] <- ev$se.exprs
                } else if (warnings) {
                  warning(paste("Error with affyid:", id))
                }
                ## no need for an 'else' branching since exp.mat was initialized with NA
                
              }
              
              options(show.error.messages = TRUE)
              on.exit(NULL)
              
              if (verbose) cat("\n")

              ## instance exprSet
              ##if (verbose) cat("instancianting an exprSet.....")
              dimnames(exp.mat) <- list(ids, sampleNames(x))
              dimnames(se.mat) <- list(ids, sampleNames(x))
              eset <- new("exprSet",
                          exprs=exp.mat,
                          se.exprs=se.mat, ##this changed
                          phenoData=phenoData(x))
                          ##description=description(x)
                          ##annotation=annotation(x),
                          ##notes=notes(x))
              ##if (verbose) cat(".....done.\n")
              
              return(eset)
            },
            where=where)