[BioC] print layout for Agilent data?

[Jianping Jin]

Hi John,

This is my first to handle the Agilent 4x44k arrays. Yes you are right. My 
collaborator ran 9 chips and sent me 36 separate files. For "read.maimages" 
they should serve as individual data files to read in just like regular 
arrays. Am I right? Is there any other file(s) which need to be read in?

best,

JP-



--On Monday, October 29, 2007 5:26 PM -0700 John Fernandes 
<jfernand at stanford.edu> wrote:

> 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
>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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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
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104, Campus
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at unc.edu