Okay I managed to debug the problem. It seemed that indexOf didn't
like my filenames because the files had parentheses in the name. But
now display(ae) fails because the path for the html file is messed up,
with backslashes ("\") instead of forward slashes ("/").
Any thoughts on this?
Thanks,
-Larry.
On Jul 2, 3:21 am, larryns <larr...@gmail.com> wrote:
> Hi,
>
> I've seen a post with this error before, but I haven't encountered a
> solution. Here is my simple script:
>
> library(aroma.affymetrix)
>
> verbose <- Arguments$getVerbose(-8, timestamp=T)
>
> # Load the annotation files
> chipType <- "MoEx-1_0-st-v1"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="core")
> cs <- AffymetrixCelSet$byName("MNSMA", cdf=cdf)
>
> # background normalization
> bc <- RmaBackgroundCorrection(cs)
> rma <- process(bc, verbose=verbose)
>
> # quantile normalization
> qn <- QuantileNormalization(rma, typesToUpdate="pm")
> print(qn)
> csN <- process(qn, verbose=verbose)
>
> # summarize by exon
> #plmEx <- ExonRmaPlm(csN, mergeGroups=F)
> #fit(plmEx, verbose=verbose)
>
> # summarize by probeset
> plm <- RmaPlm(csN)
> fit(plm, verbose=verbose)
>
> rs <- calculateResiduals(plm, verbose=verbose)
> ae <- ArrayExplorer(rs)
> setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
> process(ae, interleaved="auto", verbose=verbose)
>
> ---
> The relevant, screendump:
>
> > process(ae, interleaved="auto", verbose=verbose)
>
> 20100702 03:19:33|Generating ArrayExplorer report...
> 20100702 03:19:33| Setting up ArrayExplorer report files...
> 20100702 03:19:33| Copying template files...
> 20100702 03:19:33| Source path: /Library/Frameworks/R.framework/
> Resources/library/aroma.core/reports/includes
> 20100702 03:19:33| Destination path: reports/includes
> 20100702 03:19:33| Copying template files...done
> 20100702 03:19:33| Setting up ArrayExplorer report files...done
> 20100702 03:19:33| Updating ArrayExplorer.onChipType.js...
> 20100702 03:19:33| Source: /Library/Frameworks/R.framework/Resources/
> library/aroma.core/reports/templates/rsp/ArrayExplorer/
> ArrayExplorer.onChipType.js.rsp
> 20100702 03:19:33| Output path: reports/MNSMA/RBC,QN,RMA
> 20100702 03:19:33| Compiling RSP...
> 20100702 03:19:33| Color maps: log2,log2neg,rainbow,
> log2,log2pos,rainbow
> 20100702 03:19:33| Chip type: MoEx-1_0-st-v1,core
> Error in readCelHeader(pathname) :
> Cannot read CEL file header. File not found: NA/NA
> In addition: Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
> 20100702 03:19:33| Compiling RSP...done
> 20100702 03:19:33| Updating ArrayExplorer.onChipType.js...done
> 20100702 03:19:33|Generating ArrayExplorer report...done> traceback()
>
> 34: stop("Cannot read CEL file header. File not found: ", filename)
> 33: readCelHeader(pathname)
> 32: getHeader.AffymetrixCelFile(this)
> 31: getHeader(this)
> 30: getCdf.AffymetrixCelFile(this$files[[1]], ...)
> 29: getCdf(this$files[[1]], ...)
> 28: getCdf.AffymetrixCelSet(this)
> 27: getCdf(this)
> 26: clearCache.AffymetrixCelSet(res)
> 25: NextMethod(generic = "clearCache", object = this, ...)
> 24: clearCache.ResidualSet(res)
> 23: clearCache(res)
> 22: extract.GenericDataFileSet(X[[1L]], ...)
> 21: FUN(X[[1L]], ...)
> 20: lapply.default(dsList, FUN = extract, files, ...)
> 19: lapply(dsList, FUN = extract, files, ...)
> 18: extract.GenericDataFileSetList(this, ..., onDuplicated = "error")
> 17: extract(this, ..., onDuplicated = "error")
> 16: getFileList.GenericDataFileSetList(this, ii, ...)
> 15: getFileList(this, ii, ...)
> 14: getFullNames.AromaMicroarrayDataSetTuple(setTuple)
> 13: getFullNames(setTuple)
> 12: eval(expr, envir, enclos)
> 11: eval(rExpr, envir = envir)
> 10: sourceRsp.default(file = pathname, response = response, ...)
> 9: sourceRsp(file = pathname, response = response, ...)
> 8: rspToHtml.default(pathname, path = NULL, outFile = outFile, outPath
> = outPath,
> overwrite = TRUE, envir = env)
> 7: rspToHtml(pathname, path = NULL, outFile = outFile, outPath =
> outPath,
> overwrite = TRUE, envir = env)
> 6: updateOnChipTypeJS.ArrayExplorer(this, ...)
> 5: updateOnChipTypeJS(this, ...)
> 4: setup.ArrayExplorer(this, ..., verbose = less(verbose))
> 3: setup(this, ..., verbose = less(verbose))
> 2: process.ArrayExplorer(ae, interleaved = "auto", verbose = verbose)
> 1: process(ae, interleaved = "auto", verbose = verbose)> sessionInfo()
>
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] preprocessCore_1.10.0 Biobase_2.8.0
> aroma.affymetrix_1.6.0
> [4] aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0
> [7] aroma.core_1.6.0 aroma.light_1.16.0
> matrixStats_0.2.1
> [10] R.rsp_0.3.6 R.cache_0.3.0
> R.filesets_0.8.2
> [13] digest_0.4.2 R.utils_1.4.2
> R.oo_1.7.3
> [16] affy_1.26.1 R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0 tools_2.11.1
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
> possible
>
> ---
>
> From some (really) preliminary debugging, it looks like getPathname is
> failing because this.$pathname is NA. So I think the pathnames aren't
> being stored? If someone could please shed some light on this issue,
> I'd be very grateful.
>
> Thanks for any help,
> -Larry.
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