Hi Neel, 

 

I think your problem with the filtering function, is not the filtering itself but when the function tries to write an output. I am modifying this, so the user can choose whether or not they want to have an output file in the filtering step. In the meantime, can you tell me what you have in? 

names(dd), 

names(dd$genes)

names(dd$genes)

names(dd$other)

 

What version of the Extractor are you using? 

 

 

 

p.- 

 

De: Neel Aluru [mailto:naluru@whoi.edu] 
Enviado el: Wednesday, June 16, 2010 10:54 PM
Para: Richard Friedman; Pedro López Romero; bio c bioconductor
Asunto: Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.

 

Hi Rich,

Did you try filtering probes using FilterMicroRna function after removing the two columns. I am having difficulty in filtering probes. 

Thanks,
Neel

At 04:19 PM 6/16/2010, Richard Friedman wrote:



Dear Pedro and List,

        My text files form Agilent  Mouse miRNA Microarray Release 12.0  
G4471A-021828 has two extra columns which are not
in  GSE19232  Agilent human microRNA array v 2.0 (G44708) - "start"  
and "sequence". When these are deleted
AgiMicroRNA  works. I do not know if this is due to the array or  
software or processing options on the software.
This clears up the problem with maMicroRna( which i have been writing  
you about. It would be nice if
this could be taken into  automatically in a future version of  
AgiMicroRNA, but this solves my porblem for now.

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
George Scithers

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Neel Aluru Ph.D.
Post doctoral Scholar
Biology Department
Redfield 304 (MS#32)
Woods Hole Oceanographic Institution
Woods Hole MA 02543 USA
Phone: (508) 289-3607 [Office]
774-392-3727 [Cell] 
RID: A-7237-2009 




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