Hello,

 

My goal is to preprocess and normalize Affy Mouse Gene 1.0 ST arrays but am having difficulty doing so in R.

 

I have successfully built my own annotation package, which has the name "pd.mogene.1.0.st.v1".  However, after loading the package and reading in my CEL files, it does not automatically annotate the dataset and outputs the following:

 

> data
AffyBatch object
size of arrays=1050x1050 features (14 kb)
cdf=pd.mogene.1.0.st.v1 (??? affyids)
number of samples=8
Error in getCdfInfo(object) :
 Could not obtain CDF environment, problems encountered:
Specified environment does not contain pd.mogene.1.0.st.v1
Library - package pd.mogene.1.0.st.v1cdf not installed
Data for package affy did not contain pd.mogene.1.0.st.v1cdf
Bioconductor - could not connect
In addition: Warning messages:
1: In readLines(biocURL) :
 cannot open: HTTP status was '503 Service Unavailable'
2: missing cdf environment! in show(AffyBatch)
3: In readLines(biocURL) :
 cannot open: HTTP status was '503 Service Unavailable'

 

 

For some reason, the package names are not synchronized but I cannot figure out how to rebuild the package by specifying the name.  This is the code I used to build the package:

 

pgfFile <- "MoGene-1_0-st-v1.r3.pgf"

clfFile <- "MoGene-1_0-st-v1.r3.clf"

transFile <- "MoGene-1_0-st-v1.na26.mm9.transcript.csv"

probeFile <- "MoGene-1_0-st-v1.probe.tab"

pkg <- new("AffyGenePDInfoPkgSeed", author = "em", email =

"mathee@mail.nih.gov", version = "0.0.1", genomebuild = "thegenomebuilddate",

biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,

transFile = transFile, probeFile = probeFile)

makePdInfoPackage(pkg,destDir=".")

 

Thanks in advance for any input you can give me on this!

 

Ewy

 

Ewy Mathé, Ph. D.

Laboratory of Human Carcinogenesis

National Cancer Institute, NIH

37 Convent Drive

Building 37, Room 3068

Bethesda, MD  20892-4255

Tel: 301-496-5835

Fax: 301-496-0497

 


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