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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