Hi,
I was trying to run this :
http://www.aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo/
to create a mighty cdf file for HuGene-2_0-st affymetrix array from this
bioconductor annotation package
<http://www.bioconductor.org/packages/release/data/annotation/html/pd.hugene.2.0.st.html>
.
When running the example code (after installing the appropriate packages) :
library("aroma.affymetrix")
library("pd.hugene.1.0.st.v1")
pathname <- writeCdf(pd.hugene.1.0.st.v1, tags =
"pd.hugene.1.0.st.v1,HB20110111", overwrite = TRUE)
I obtained this error:
> pathname <- writeCdf(pd.hugene.1.0.st.v1, tags=
"pd.hugene.1.0.st.v1,HB20110111", overwrite=TRUE)
Loading required namespace: pdInfoBuilder
Generating CDF file from Platform Design (PD) package...
Platform Design (PD) package: pd.hugene.1.0.st.v1
Output path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf
Pathname to generated CDF: annotationData/chipTypes/HuGene-1_0-st-v1/HuGene
-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf
Chip type: HuGene-1_0-st-v1
Tags: pd.hugene.1.0.st.v1,HB20110111
Chip type dimensions: 1050x1050
Total number of cells (probes): 1102500
Querying Platform Design database...
Units by: transcript
Names by: fsetid
Available database tables:
[1] "chrom_dict" "core_mps" "featureSet" "level_dict" "pmfeature"
[6] "table_info" "type_dict"
SQL query:
SELECT DISTINCT
-- fid,
meta_fsetid AS probeset_id,
atom,
x,
y
FROM pmfeature
INNER JOIN core_mps USING(fsetid)
ORDER BY probeset_id, atom
'data.frame': 861493 obs. of 4 variables:
$ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502
7892502 7892502 7892503 7892503 ...
$ atom : int 1 2 3 5 7 10 11 12 13 14 ...
$ x : int 870 28 638 888 108 411 918 958 928 495 ...
$ y : int 110 899 469 863 984 622 657 949 361 447 ...
'data.frame': 861493 obs. of 4 variables:
$ probeset_id: int 7892501 7892501 7892501 7892501 7892502 7892502
7892502 7892502 7892503 7892503 ...
$ atom : int 1 2 3 5 7 10 11 12 13 14 ...
$ x : int 870 28 638 888 108 411 918 958 928 495 ...
$ y : int 110 899 469 863 984 622 657 949 361 447 ...
Number of cells (probes) in PD database: 861493 (78.14%) of 1102500
Querying Platform Design database...done
Number of units: 33297
Unit names: 7892501, 7892502, 7892503, ..., 8180418
Average number of cells per units: 25.87
List of 3
$ 7892501:'data.frame': 4 obs. of 4 variables:
..$ probeset_id: int [1:4] 7892501 7892501 7892501 7892501
..$ atom : int [1:4] 1 2 3 5
..$ x : int [1:4] 870 28 638 888
..$ y : int [1:4] 110 899 469 863
$ 7892502:'data.frame': 4 obs. of 4 variables:
..$ probeset_id: int [1:4] 7892502 7892502 7892502 7892502
..$ atom : int [1:4] 7 10 11 12
..$ x : int [1:4] 108 411 918 958
..$ y : int [1:4] 984 622 657 949
$ 7892503:'data.frame': 4 obs. of 4 variables:
..$ probeset_id: int [1:4] 7892503 7892503 7892503 7892503
..$ atom : int [1:4] 13 14 17 18
..$ x : int [1:4] 928 495 316 840
..$ y : int [1:4] 361 447 686 698
Error in affxparser::writeCdf(...) :
unused argument (pathname =
"annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,pd.hugene.1.0.st.v1,HB20110111.cdf"
)
I am a simple R user and not an advanced package-maker wizard, so what I
will say next is likely to be absurd, but:
1) AffyGenePDInfo.writeCdf.R source code:
setMethodS3("writeCdf", "AffyGenePDInfo", function(this, tags=c("*"),
unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"), path=NULL,
overwrite=FALSE, verbose=TRUE, ...) {
[...]
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Writing CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathname <- .writeCdf(ffs, pathname=pathname, overwrite=overwrite, verbose
=less(verbose));
[...]
}
setMethodS3("writeCdf", "PDInfoList", function(ffs, pathname, overwrite=
FALSE, ..., verbose=TRUE) {
[...]
pathnameT <- pushTemporaryFile(pathname, verbose=verbose);
.writeCdf(pathnameT, cdfheader=cdfHeader, cdf=cdfList,
cdfqc=NULL, verbose=verbose, overwrite=overwrite);
[...]
}
I am totaly confused by what is this .writeCdf function. Is it the writeCdf
function from affxparser package?
2) affxparser::writeCdf first parameter is fname and not pathname. Hence
the error?
writeCdf(fname, cdfheader, cdf, cdfqc, overwrite=FALSE, verbose=0)
3) aroma is loading affxparser itself, and is masking the writeCdf function:
Loading required package: affxparser
Attaching package: âaffxparserâ
The following object is masked from âpackage:aroma.affymetrixâ:
writeCdf
and the annotation package:
Attaching package: âoligoâ
The following object is masked _by_ package:aroma.affymetrix:
writeCdf
Reversing the order of package loading did not solved the issue.
I am having the same issue when generating the cdf for the HuGene-2_0-st
array.
Thanks,
Guillaume
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Scientific Linux release 6.5 (Carbon)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] pd.hugene.1.0.st.v1_3.14.1 Biobase_2.28.0
[3] oligoClasses_1.30.0 RSQLite_1.0.0
[5] DBI_0.3.1 Biostrings_2.36.3
[7] XVector_0.8.0 IRanges_2.2.5
[9] S4Vectors_0.6.2 BiocGenerics_0.14.0
[11] aroma.light_2.4.0 aroma.affymetrix_2.13.2
[13] aroma.core_2.13.1 R.devices_2.13.0
[15] R.filesets_2.8.0 R.utils_2.1.0
[17] R.oo_1.19.0 oligo_1.32.0
[19] affxparser_1.40.0 R.methodsS3_1.7.0
loaded via a namespace (and not attached):
[1] BiocInstaller_1.18.4 pdInfoBuilder_1.32.1 GenomeInfoDb_1.4.1
[4] base64enc_0.1-3 iterators_1.0.7 tools_3.2.0
[7] zlibbioc_1.14.0 digest_0.6.8 aroma.apd_0.6.0
[10] bit_1.1-12 preprocessCore_1.30.0 R.cache_0.10.0
[13] ff_2.2-13 foreach_1.4.2 R.rsp_0.20.0
[16] PSCBS_0.44.0 DNAcopy_1.42.0 codetools_0.2-14
[19] matrixStats_0.14.2 GenomicRanges_1.20.5 splines_3.2.0
[22] R.huge_0.9.0 Cairo_1.5-8 affyio_1.36.0
--
--
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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
