[BioC] Affymetrix US Rice Gene Strip 1.1

[James W. MacDonald]

Hi Nick,

You can't use the affy package for this analysis. Instead you need to 
use either oligo or xps. I can't help with xps, but perhaps Christian 
Stratowa will give you some hints.

For oligo you will need to build some packages. First, get the files here:

http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RUSGene-1_1-st-v1/RUSGene-1_1-st_rev2.zip
http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RUSGene-1_1-st-v1/RUSGene-1_1-st-v1.design-time.20130417.zip

and unzip somewhere. You then need to build a pd.info package. So 
install pdInfoBuilder using biocLite(), and then follow the instructions 
here:

https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html

You essentially want to be able to tell pdInfoBuilder where these files are:

RUSGene-1_1-st.mps
RUSGene-1_1-st.pgf
RUSGene-1_1-st.clf
RUSGene-1_1-st-v1.design-time.20130417.probeset.csv
RUSGene-1_1-st-v1.design-time.20130417.transcript.csv

You can just pull them out of the unzipped files and put them somewhere 
convenient, and then follow what Kamila did in the above referenced BioC 
mail message. Once you have built the package you will have to install 
it. Usually something like

install.packages("<filename goes here>", repos=NULL, type="source")

will do the trick.

Best,

Jim




On 5/8/2013 5:28 PM, Nicholas Lawson [guest] wrote:
> Hello,
> 	I am trying to use bioconductor to run analysis on my Affymetrix Gene Strip array data. I have loaded just about everything I can find to load, libraries and packages. However, I keep getting an error in getCdfInfo(object): Specified environment does not contain RUSGene-1_1-st Library - package rusgene11stcdf not installed. Then I try to run biocLite(rusgene11stcdf) and it tells me that 'rusgene11stcdf' is not available. I tried downloading a folder from affymetrix that has info on the RUS gene st array but there are no cdc files in that. Please help!
>
> Thanks,
> Nick Lawson
>
>   -- output of sessionInfo():
>
>> eset<- justRMA()
> Error in getCdfInfo(object) :
>    Could not obtain CDF environment, problems encountered:
> Specified environment does not contain RUSGene-1_1-st
> Library - package rusgene11stcdf not installed
> Bioconductor - rusgene11stcdf not available
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099