Question: HuGene 2.0 ST CDF files and xps
0
gravatar for Alison Ziesel
4.9 years ago by
United States
Alison Ziesel60 wrote:

Hello all,

I had written to the list earlier this month regarding a function of the oligo package ("Oligo package: paCalls question"), and mentioned I had had difficulty getting an alternate package, xps, installed. After setting the problem aside for a period, I've since been able to correctly compile and install the prerequisite root software and xps.

The arrays used in this current study are Human Gene 2.0 ST arrays. Following the xps introduction PDF, and in particular Appendix A1 (Importing chip definition and annotation files) I've been trying to generate a root scheme file for this platform. Unfortunately I've been completely stymied when looking for the CDF file for that platform. Is there an available root scheme file out there, or has my Google-fu completely failed to turn up a CDF for this chip? I can find CDFs for the human 1.0 and 1.1 chips.

I CC'd Dr. Stratowa on this, after he was kind enough to reach out on my last help request. I'd be very grateful for any information on where I can either obtain the CDF file or a root scheme for this chip set. Thank you in advance!

alison

Alison Ziesel
Department of Ophthalmology, Emory University
aziesel@emory.edu

xps hugene20 • 1.8k views
ADD COMMENTlink modified 4.9 years ago by cstrato3.9k • written 4.9 years ago by Alison Ziesel60
Answer: HuGene 2.0 ST CDF files and xps
2
gravatar for cstrato
4.9 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:

Dear Alison,

Please note that for whole genome arrays Affymetrix has replaced CDF-files with PGF-files and CLF-files.

You can download these files and the necessary annotation files from Affymetrix:
- go to www.affymetrix.com
- select Support -> Microarray Solutions
- in 'Select A Product' select 'Human Gene 2.0 ST Array'
- select 'Software & Data'
- press 'Go' button
- from Library Files download:
  - 'Human Gene 2.0 ST Array, Analysis', i.e. HuGene-2_0-st_rev1.zip
- from 'Current NetAffx Annotation Files' download:
  - HuGene-2_0-st-v1.na34.hg19.probeset.csv.zip
  - HuGene-2_0-st-v1.na34.hg19.transcript.csv.zip

The file 'HuGene-2_0-st_rev1.zip' contains the files:
- HuGene-2_0-st.pgf
- HuGene-2_0-st.clf

In the script 'xps/examples/script4schemes.R' you can find the code how to create the root scheme file for the HuGene-2.0 array.

Best regards,
Christian
 

ADD COMMENTlink written 4.9 years ago by cstrato3.9k

Thank you for your swift reply!

I had found the .pgf, .clf, and .csv files earlier, but was trying to use import.expr.scheme rather than import.exon.scheme as described in the script4schemes.R file. Thank you so much for clearing this up for me, I'm very grateful!

 

alison

ADD REPLYlink written 4.9 years ago by Alison Ziesel60
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