The block-level files I received are indeed txt files. When I open  
them by a txt editor just to check, it has the block info as the  
first column.

After I inputed them with a target.ext file, the block info is still  
there. Such as:

 > RGH$genes[1:5,]
   Block Row Column              ID            Name
1     1   1      1 GE_BrightCorner GE_BrightCorner
2     1   1      2 GE_BrightCorner GE_BrightCorner
3     1   1      3      DarkCorner      DarkCorner
4     1   1      4      DarkCorner      DarkCorner
5     1   1      5      DarkCorner      DarkCorner

So, is it possible your files are not complete?

For normalization, I used the same command as Sean suggested:

MAHWC<-normalizeWithinArrays(RGHWC, method="loess")

It worked just fine.

Yong


On Oct 30, 2007, at 9:50 AM, Jianping Jin wrote:

> 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@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@email.unc.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 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



	[[alternative HTML version deleted]]

