[BioC] inquiry for CDF file

[James W. MacDonald]

Hi Hyeong-Min,

Lee, Hyeong-min wrote:
> Hello.
> I'm looking for "mogene10stv1cdf" I couldn't find it on the metadata.html.
> Could you please tell me where I can get it? Thank you for your time.

Unfortunately, we don't as yet supply the cdf file for this chip type.

There are a couple of ways you can analyze these data, but none involves 
the canonical makecdfenv/affy pipeline.

You can use the successor to makecdfenv/affy, which is the 
pdInfoBuilder/oligo pipeline (more to follow on this), or the xps 
package. Non-BioC software includes aroma.affymetrix and Expression 
Console (Affymetrix's own software).

To use oligo to do the analysis you will first need to create a pdInfo 
package. This package replaces all of the cdf, probe and annotation 
packages that you may be used to. In order to build this package you 
will need to download the library files (the first one on this page: 
http://www.affymetrix.com/support/technical/byproduct.affx?product=mogene-1_0-st-v1), 
the probe file in tabular format, and the transcript cluster annotation 
csv file (both of which are found at the above URL).

You then have to create a 'AffyGenePDInfoPkgSeed' object which you can 
then use to build the package. The help page for this doesn't really 
cover this sort of thing, so here is an example of how you would do so:

pgfFile <- "MoGene-1_0-st-v1.r3.pgf"
clfFile <- "MoGene-1_0-st-v1.r3.clf"
transFile <- "MoGene-1_0-st-v1.na24.mm8.transcript.csv"
probeFile <- "MoGene-1_0-st-v1.probe.tab"

pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email = 
"e at mail.net", version = "0.0.1", genomebuild = "thegenomebuilddate",
biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, 
transFile = transFile, probeFile = probeFile)

makePdInfoPackage(pkg)

At this point you need to install the package. In any case, this is done 
at a terminal prompt (or DOS prompt on Windows) using

R CMD INSTALL thepackage

You may also need to point to your library directory as well, using 
something like

R CMD INSTALL -l /path/to/lib thepackage

If you are on linux, this Will Just Work (tm). However, if you are on 
Windows or MacOS, you will need to get set up to build packages. Luckily 
this isn't nearly as involved as in the past. See the R Installation and 
Administration manual

http://cran.r-project.org/doc/manuals/R-admin.html

for your particular OS.

Best,

Jim



>  
> Best
>  
> Hyeong-Min Lee
> Ph.D. candidate
> Program in Neurobiology
> Dept. Biomedical Sciences
> College of Medicine, FSU
> Lab; 850-645-2922
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623