ArrayExplorer problem
Randy Gobbel
ArrayExplorer. I'm running on an 8 CPU (Xeon) Mac Pro, OS 10.5.8,
EBImage and supporting software just installed from scratch:
> rs <- calculateResidualSet(plm)
> ae <- ArrayExplorer(rs)
> setColorMaps(ae, c('log2,log2neg,rainbow','log2,log2pos,rainbow'))
> process(ae, interleaved='auto')
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
> 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")
1: process(ae, interleaved = "auto")
> rs
ResidualSet:
Name: all
Tags: RBC,QN,RMA
Path: plmData/all,RBC,QN,RMA/Hs133P_Hs_REFSEQ
Platform: Affymetrix
Chip type: Hs133P_Hs_REFSEQ
Number of arrays: 9
Names: EA08034_98020_H133+_MCCW199, EA08034_98021_H133+_SKINW199, ...,
EA08034_98031_H133+_PN-1NN2
Time period: 2010-01-20 15:59:10 -- 2010-01-20 15:59:28
Total file size: 116.30MB
RAM: 0.01MB
Parameters: (probeModel: chr "pm")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Hs133P_Hs_REFSEQ
Filename: Hs133P_Hs_REFSEQ.cdf
Filesize: 15.21MB
Chip type: Hs133P_Hs_REFSEQ
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1164x1164
Number of cells: 1354896
Number of units: 25102
Cells per unit: 53.98
Number of QC units: 9
Any suggestions? Everything else seems to be working fine at this
point.
Henrik Bengtsson
what does sessionInfo() report after getting the error?
/Henrik
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
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Randy Gobbel
R version 2.10.1 (2009-12-14)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] affyio_1.14.0 Biobase_2.6.1
aroma.affymetrix_1.4.0 aroma.apd_0.1.7 affxparser_1.18.0
R.huge_0.2.0
[7] aroma.core_1.4.0 aroma.light_1.15.1
matrixStats_0.1.8 R.rsp_0.3.6 R.filesets_0.7.0
digest_0.4.2
[13] R.cache_0.2.0 R.utils_1.3.0
R.oo_1.6.6 affy_1.24.2 R.methodsS3_1.1.0
loaded via a namespace (and not attached):
[1] preprocessCore_1.8.0 tools_2.10.1
On Jan 25, 6:21 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
Henrik Bengtsson
this might have to do we recent updated in aroma.affymetrix v1.4.0. What does
print(getFullNames(rs))
print(getNames(rs))
print(unique(getNames(rs)))
give?
/Henrik
Randy Gobbel
[1] "EA08034_98020_H133+_MCCW199,residuals"
"EA08034_98021_H133+_SKINW199,residuals"
"EA08034_98022_H133+_MCCW173,residuals"
[4] "EA08034_98024_H133+_MCCW184,residuals"
"EA08034_98026_H133+_PN-1TT1,residuals"
"EA08034_98027_H133+_PN-1TT2,residuals"
[7] "EA08034_98028_H133+_PN-1TT3,residuals"
"EA08034_98030_H133+_PN-1NN1,residuals"
"EA08034_98031_H133+_PN-1NN2,residuals"
> print(getNames(rs))
[1] "EA08034_98020_H133+_MCCW199" "EA08034_98021_H133+_SKINW199"
"EA08034_98022_H133+_MCCW173" "EA08034_98024_H133+_MCCW184"
"EA08034_98026_H133+_PN-1TT1"
[6] "EA08034_98027_H133+_PN-1TT2" "EA08034_98028_H133+_PN-1TT3"
"EA08034_98030_H133+_PN-1NN1" "EA08034_98031_H133+_PN-1NN2"
> print(unique(getNames(rs)))
[1] "EA08034_98020_H133+_MCCW199" "EA08034_98021_H133+_SKINW199"
"EA08034_98022_H133+_MCCW173" "EA08034_98024_H133+_MCCW184"
"EA08034_98026_H133+_PN-1TT1"
[6] "EA08034_98027_H133+_PN-1TT2" "EA08034_98028_H133+_PN-1TT3"
"EA08034_98030_H133+_PN-1NN1" "EA08034_98031_H133+_PN-1NN2"
On Jan 26, 5:04 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> Hi,
>
Randy Gobbel
chromosome bias correction vignette, and seem to have run into the
same problem:
> M <- NULL
> for (kk in 1:nbrOfArrays(cbs)) {
+ rawCNs <- extractRawCopyNumbers(cbs, array=kk, chromosome=23);
+ rawCNs <- as.data.frame(rawCNs)$cn;
+ M <- cbind(M, rawCNs);
+ }
Error in readCelHeader(pathname) :
Cannot read CEL file header. File not found: NA/NA
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
> traceback()
24: stop("Cannot read CEL file header. File not found: ", filename)
23: readCelHeader(pathname)
22: getHeader.AffymetrixCelFile(this)
21: getHeader(this)
20: getCdf.AffymetrixCelFile(this$files[[1]], ...)
19: getCdf(this$files[[1]], ...)
18: getCdf.AffymetrixCelSet(this)
17: getCdf(this)
16: clearCache.AffymetrixCelSet(res)
15: NextMethod(generic = "clearCache", object = this, ...)
14: clearCache.ChipEffectSet(res)
13: clearCache(res)
12: extract.GenericDataFileSet(X[[1L]], ...)
11: FUN(X[[1L]], ...)
10: lapply.default(dsList, FUN = extract, files, ...)
9: lapply(dsList, FUN = extract, files, ...)
8: extract.GenericDataFileSetList(this, ..., onDuplicated = "error")
7: extract(this, ..., onDuplicated = "error")
6: getFileList.GenericDataFileSetList(cesTuple, array, ..., verbose =
less(verbose,
1))
5: getFileList(cesTuple, array, ..., verbose = less(verbose, 1))
4: getDataFileMatrix.CopyNumberChromosomalModel(this, array = array,
verbose = less(verbose, 5))
3: getDataFileMatrix(this, array = array, verbose = less(verbose,
5))
2: extractRawCopyNumbers.CopyNumberChromosomalModel(cbs, array = kk,
chromosome = 23)
1: extractRawCopyNumbers(cbs, array = kk, chromosome = 23)
Henrik Bengtsson
I'm traveling, but I hope I'll have time to look into this and other
questions on the list by end of next.
/H
Henrik Bengtsson
I managed to reproduce this when using the same names as you. It
turns out to be a bug causing indexOf(ds, "foo+bar") of a data set
'ds' to return NA when the requested name contains a '+' symbol. The
reason was that the '+' was parsed as a regular expression symbol.
I've fixed R.filesets, where the bug is located. Until I release a
new version of R.filesets and submit it to CRAN, you can use the
following patch to R.filesets:
# INSTALL
library("aroma.affymetrix");
downloadPackagePatch("R.filesets");
When you've done this once, the patch will be available in all future
R sessions. It will uninstall itself when you later install the new
R.filesets version.
Let me know if this works.
/Henrik
Randy Gobbel
trouble with the sex chromosome bias correction vignette, so maybe
it's not the same problem after all, though the symptom:
("Error in readCelHeader(pathname) :
Cannot read CEL file header. File not found: NA/NA")
...seems the same. I'm re-running the SNP analysis from scratch, and
will start a new discussion thread if I continue to run into problems.
One oddity, it seems that for me, downloadPackagePatch is not being
sticky, and I've had to rerun it with every new session. The details
are a bit confused, as I'm trying to do several things at once, plus
running both 32- and 64-bit versions of R, since I've not been able to
get everything working in 64-bit mode, so it may be that I've done
something wrong, just wanted to note that that's what I'm seeing.
-Randy
On Feb 7, 6:11 am, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
Henrik Bengtsson
On Tue, Feb 9, 2010 at 7:37 PM, Randy Gobbel <randy....@gmail.com> wrote:
> This does seem to fix the ArrayExplorer computation. I'm still having
> trouble with the sex chromosome bias correction vignette, so maybe
> it's not the same problem after all, though the symptom:
>
> ("Error in readCelHeader(pathname) :
> Cannot read CEL file header. File not found: NA/NA")
>
> ...seems the same. I'm re-running the SNP analysis from scratch, and
> will start a new discussion thread if I continue to run into problems.
I cannot reproduce this, but I am also not sure where the above
occurs. Please provide full details of what you are doing and the
full traceback.
>
> One oddity, it seems that for me, downloadPackagePatch is not being
> sticky, and I've had to rerun it with every new session. The details
> are a bit confused, as I'm trying to do several things at once, plus
> running both 32- and 64-bit versions of R, since I've not been able to
> get everything working in 64-bit mode, so it may be that I've done
> something wrong, just wanted to note that that's what I'm seeing.
You are correct - I forgot that it is only for aroma.* packages that
the patches are loaded automatically when the package is loaded. You
need to do:
library("aroma.affymetrix");
patchPackage("R.filesets");
In the next release of aroma.*, patches of R.filesets will be loaded
automatically.
/Henrik