Dear James,

Thank you so much for your reply. However, I would like to ask for R script
(in sequence wise) to install MarGene 1.0st array library files into R
environment.

Kindly mention the R script for installation of MarGene 1.0st library files

Thanks

Dhanjit


On Mon, Oct 28, 2013 at 7:20 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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<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<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<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<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<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.
>>
>> ______________________________**_________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<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
>



-- 
**
*---------------------------------------------------------------*
*DR DHANJIT KUMAR DAS*
Scientist C
Genetic Research Centre
National Institute for Research in Reproductive Health
JM Street, Parel
Mumbai - 400 012
Phone: 022-24192109 / 2145
Fax: 022-24147843

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