Hi,
thank you. I can reproduce this. Explanation and fix below.
On Fri, Aug 14, 2015 at 5:27 PM, Guillaume Devailly wrote:
> 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.
>
> 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)
You did a pretty good job nailing this one down. The .writeCdf() is a
light-weig
