[BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment

James W. MacDonald jmacdon at uw.edu
Mon Oct 28 14:50:27 CET 2013


You should be using either the oligo or xps package for this array. For 
oligo, you need the pdInfoBuilder package, and some files from 
Affymetrix.

You need the pgf, clf and mps files that are in this zipfile:

http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/MarGene-1_0-st_rev01/MarGene-1_0-st_rev01.zip

And you need the probeset csv file

http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2/MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv.zip

and the transcript csv file

http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2/MarGene-1_0-st-v1.na33.2.caljac3.transcript.csv.zip

and then you can make the pd.margene.1.0.st.v1 package following these 
instructions:

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

after which you can install using

install.packages("pd.margene.1.0.st.v1/", repos=NULL, type="source")

If you want to use xps there are a set of vignettes here:

http://www.bioconductor.org/packages/release/bioc/html/xps.html

and Christian Stratowa is very helpful, so you can ask questions here 
if you get stuck.

Best,

Jim




On Monday, October 28, 2013 6:12:15 AM, DR DHANJIT KUMAR DAS [guest] 
wrote:
>
> I would like to analyze data using Marmoset Gene 1.0 ST Array. While reading the CEL file into R environment, error message is showing as "Library - package margene10stcdf not installed"
>
> How to install the package MarGene-1_0st package into R environment? The R script is attached for your reference.
>
> The part No of the array is 901961.
>
>   -- output of sessionInfo():
>
>> library(affy)
>> eset.rma <- justRMA(celfile.path="C:/Dhanjit/Marmoset-Dr Uddhav/CEL FILE/")
> Error in getCdfInfo(object) :
>    Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MarGene-1_0-st
> Library - package margene10stcdf not installed
> Bioconductor - margene10stcdf not available
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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