[BioC] How can I remove control probesets from the expressionset object in gene expression analysis with Affy Human Gene 1.0ST microarray

James W. MacDonald jmacdon at uw.edu
Tue May 8 15:25:41 CEST 2012

Hi Juan,

On 5/8/2012 6:46 AM, Juan Fernández Tajes wrote:
> Dear Bioconductor subcribers:
> First of all, I apologize for using a old-resolved bioconductor´s thread:https://stat.ethz.ch/pipermail/bioconductor/2011-June/039993.html
> " Dear list,>  >  I am quite new to R as well as to microarray analysis.>  I am dealing with some gene expression analysis performed on Affymetrix Human>  Gene 1.0ST microarray.>  >  So far, I have learnt how to filtrate data using genefilter using nsFilter>  functions.>  >  Now, I would like to know how to filter out from the expressionset object all>  the control probesets (~4000) that Affymetrix includes in the microarray (for>  quality assay, normalization, background correction, etc.). However, none of>  the aforementioned functions worked for me.>  >  How can I recognize those probesets and remove them? I would like to filter>  them out before statistical analysis with limma package."
> I have been having the same problem when using oligo to analyze the data. It so happens that when I try to filter control probe IDs with nsfilter it doesn´t work properly. Do you know anyway to get around this problem?

Probably. But you don't give us anything to go on. What code did you 
use? What happened? Define 'doesn't work properly'. What is the output 
from sessionInfo()?



> Many thanks in advance
> Juan
> ---------------------------------------------------------------
> Juan Fernandez Tajes, ph. D
> Departamento de Biología Celular y Molecular
> Facultad de Ciencias-Universidade da Coruña
> Tlf. +34 981 167000 ext 2030
> e-mail: jfernandezt at udc.es
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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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