[BioC] upload multiple genelists at a time for GO or pathway enrichment

Helen Smith helen.smith-2 at manchester.ac.uk
Mon Oct 28 15:30:33 CET 2013


Hi All, 

I have a list of clusters generated through biolayout which I need to annotate for GO annotations.  I can do this one-by-one using DAVID etc but as there are 97 clusters this is a rather lengthy procedure. 
Do any of you know of any tools were you can upload multiple lists of genes to be annotated for go over-representation (or failing that pathway enrichment)?

Any help would be greatly appreciated, 
Helen

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of James W. MacDonald
Sent: 28 October 2013 13:50
To: DR DHANJIT KUMAR DAS [guest]
Cc: bioconductor at r-project.org; dasdjk at gmail.com
Subject: Re: [BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment

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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