[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 

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


And you need the probeset csv file


and the transcript csv file


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


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:


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



On Monday, October 28, 2013 6:12:15 AM, DR DHANJIT KUMAR DAS [guest] 
> 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.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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