[BioC] print layout for Agilent data?

[Jianping Jin]

Thanks Sean.

Here back to my original questions. Reading in data with "read.maimages" 
had no problems (see below)

> RG$genes[1:5,]
  Row Col Start Sequence ProbeUID ControlType       ProbeName 
GeneName
1   1   1     0                 0           1 GE_BrightCorner 
GE_BrightCorner
2   1   2     0                 1           1      DarkCorner 
DarkCorner
3   1   3     0                 1           1      DarkCorner 
DarkCorner
4   1   4     0                 1           1      DarkCorner 
DarkCorner
5   1   5     0                 1           1      DarkCorner 
DarkCorner
   SystematicName Description
1 GE_BrightCorner
2      DarkCorner
3      DarkCorner
4      DarkCorner
5      DarkCorner

But when I was trying the normalizeWithinArrays function I got an error:
Error in switch (method, loess= {: Layout argument not specified).

As you can see the RG file has already taken in the Row and Col 
information. There is no Block column however, as Agilent array has not 
designed as different blocks. That may be the reason of the error. I wanted 
to know how people handle this situation in order to carry out loess 
normalization for each array. Do we need to add a "Block" column into 
RG$genes or specify gene layout format?

best,

JJ-

--On Tuesday, October 30, 2007 10:12 AM -0400 Sean Davis 
<sdavis2 at mail.nih.gov> wrote:

> Jianping Jin wrote:
>> 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?
>
> That should do it.
>
> Sean



##################################
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