[BioC] print layout for Agilent data?

[Jianping Jin]

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