[BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.

[Richard Friedman]

Neel,

	I haven't tried filtering after removing the columns.
I seem to remember that filtering worked on the test set,
read in with the data funtion but not on my own data before
I removed the columns. I  have to give AgiMicroRNA a rest
until tomorrow afternoon (EDT) to catch up on other things.
A suggestion.

1. Download GSE19232 from GEO.
2. See if what you do works on that dataset,
	A. If it doesn't you are doing something incorrectly.
	B. If it does, try the same thing on your dataset.
		a. If it works on your setm fine.
		b. If it doesn't work on your set compare the column headings
			of GSE19232 to yorus and modify yours to conform to GSE19232.

I hope that this helps,
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 at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
George Scithers



On Jun 16, 2010, at 4:54 PM, Neel Aluru wrote:

> 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 at 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
>