[BioC] print layout for Agilent data?

[John Fernandes]

The Feature Extraction software from Agilent knows the format from the  
control file supplied by Agilent and will create 4 sets of separate  
files.  You run your analysis as if they were singly hybridized 44K  
arrays.

John


> Thanks Yong!
>
> Your way may be a good one for "normalizeWithArrays" to work in a regular
> manner. But it may be questionable if you need to apply
> "normalizeBetweenArrays". My data set used common reference design. I may
> want to carry out normalization between arrays.
>
> I read in data using "read.maimages" with source="agilent". There should be
> some standard ways by which I can run normalization within arrays. Am I
> correct?
>
> best,
>
> JJ-
>
> --On Monday, October 29, 2007 2:51 PM -0500 Yong Yin
> <yyin at watson.wustl.edu> wrote:
>
>> If you are asking how to handle different blocks in Agilent 4x44k, we
>> have had the same problem.
>>
>>
>> In brief, we have printed the same set of 44k probes on each of the 4
>> blocks, and we are applying different samples onto different blocks.
>>
>>
>> After discussing with our microarray facility, they find a way to
>> generate individual raw data file for each array using the software
>> coming with scanner. Then I just treat data generated from different
>> blocks as independent arrays.
>>
>>
>> I suggest you talk to the people running the machines. And I would love
>> to hear others' experiences.
>>
>>
>> Best,
>>
>>
>> Yong
>>
>>
>>  
>>
>>
>> On Oct 29, 2007, at 2:19 PM, Jianping Jin wrote:
>>
>>
>> Dear list,
>>
>>
>> When I was trying the normalizeWithinArrays function of limma I got an 
>> error: Error in switch (method, loess = {: Layout argument not
>> specified). 
>> I was using an Agilent 4 x 44k data set and knew the Agilent printer has 
>> only one block (Row and Col having been taken already). How can I do
>> loess 
>> normalization for each slide? Should I add a Block column into the RG,
>> the 
>> data read-in file in order to do normalizaWithinArrays?
>>
>>
>> Another question is that is there any easy way I can remove all control 
>> spots from all data files?
>>
>>
>> Appreciate your help!
>>
>>
>> JJ
>>
>>
>> ##################################
>> Jianping Jin Ph.D.
>> Bioinformatics scientist
>> Center for Bioinformatics
>> Room 3133 Bioinformatics building
>> CB# 7104
>> University of Chapel Hill
>> Chapel Hill, NC 27599
>> Phone: (919)843-6105
>> FAX:   (919)843-3103
>> E-Mail: jjin at email.unc.edu
>>
>>
>> _______________________________________________
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>>
>>
>>
>>
>>
>>
>> Yong Yin, Ph.D.
>>
>>
>> Senior Scientist
>> Genome Sequencing Center
>> Washington University School of Medicine, Campus box 8501
>> 4444 Forest Park
>> Saint Louis, MO 63108
>>
>>
>> Tel: (314) 286-1415
>>
>
>
>
> ##################################
> Jianping Jin Ph.D.
> Bioinformatics scientist
> Center for Bioinformatics
> Room 3133 Bioinformatics building
> CB# 7104
> University of Chapel Hill
> Chapel Hill, NC 27599
> Phone: (919)843-6105
> FAX:   (919)843-3103
> E-Mail: jjin at email.unc.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> http://news.gmane.org/gmane.science.biology.informatics.conductor