[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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