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@email.unc.edu
>
> _______________________________________________
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> Search the archives: http://news.gmane.org/ 
> gmane.science.biology.informatics.conductor
>

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



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