Hi, I am trying to use the pdInfoBuilder package to build design info package for the Affy Human Gene ST 1.0 arrays. I have several questions and appreciate if someone can share their knowledge. I used R 2.11/BioC 2.6, but had the same problem with R 2.10/BioC 2.5. 1. I had to specify the coreMps when creating the seed. Otherwise got a "coreMps" not found error, which was different from what the manual says. I did not see any information about this coreMps parameter. 2. When I added coreMps, makePdInfoPackage ran okay, with output slightly different from the manual, and also two warning messages: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' When I tried to use it in the oligo package with "read.celfiles" or simply trying to load the newly created pd.hugene.1.0.st.v1 package, I got and error saying: "Error in library(pd.hugene.1.0.st.v1) : 'pd.hugene.1.0.st.v1' is not a valid installed package ". I can not tell what I did wrong. 3. I understand that there is a package called "pd.hugene.1.0.st.v1" that you can download from the bioC metadata, will this be the same if my code had worked? 4. The pgf, clf, and mps files that I can find from the affy site are for r4 version i.e. the probeset info, and matched the HuGene- 1_0-st-v1.na30.1.hg19.probeset.csv file. I also wanted to get the r3 version i.e. the transcript level info to use with the HuGene- 1_0-st-v1.na30.hg19.transcript.csv file, but cannot find it. Is there any other way to get the transcript level data summarization? Thank you very much for your help! Yiwen He NIH/CIT/BIMAS > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.12.0 oligo_1.12.2 oligoClasses_1.10.0 affxparser_1.20.0 RSQLite_0.9-1 [6] DBI_0.2-5 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 Biostrings_2.16.6 IRanges_1.6.8 preprocessCore_1.10.0 splines_2.11.1 [6] tools_2.11.1 > library(pdInfoBuilder) > mydir="." > pgf=list.files(mydir, pattern=".pgf", full.names=T) > clf=list.files(mydir, pattern=".clf", full.names=T) > mps=list.files(mydir, pattern=".mps", full.names=T) > prob="HuGene-1_0-st-v1.na30.1.hg19.probeset.csv" > trsc="HuGene-1_0-st-v1.na30.hg19.transcript.csv" > seed.1=new("AffyGenePDInfoPkgSeed", pgfFile=pgf, clfFile=clf, probeFile=prob, coreMps=mps) > makePdInfoPackage(seed.1, destDir=".") ====================================================================== ============================================== Building annotation package for Affymetrix Gene ST Array PGF.........: HuGene-1_0-st-v1.r4.pgf CLF.........: HuGene-1_0-st-v1.r4.clf Probeset....: HuGene-1_0-st-v1.na30.1.hg19.probeset.csv Core MPS....: HuGene-1_0-st-v1.r4.mps ====================================================================== ============================================== Parsing file: HuGene-1_0-st-v1.r4.pgf... OK Parsing file: HuGene-1_0-st-v1.r4.clf... OK Creating initial table for probes... OK Creating dictionaries... OK Parsing file: HuGene-1_0-st-v1.na30.1.hg19.probeset.csv... OK Parsing file: HuGene-1_0-st-v1.r4.mps... OK Creating package in ./pd.hugene.1.0.st.v1 Inserting 250 rows into table chrom_dict... OK Inserting 5 rows into table level_dict... OK Inserting 8 rows into table type_dict... OK Inserting 257430 rows into table core_mps... OK Inserting 257430 rows into table featureSet... OK Inserting 861493 rows into table pmfeature... OK Counting rows in chrom_dict Counting rows in core_mps Counting rows in featureSet Counting rows in level_dict Counting rows in pmfeature Counting rows in type_dict Creating index idx_pmfsetid on pmfeature... OK Creating index idx_pmfid on pmfeature... OK Creating index idx_fsfsetid on featureSet... OK Creating index idx_core_meta_fsetid on core_mps... OK Creating index idx_core_fsetid on core_mps... OK Saving DataFrame object for PM. Done. Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' [[alternative HTML version deleted]]