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'

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