[BioC] print layout for Agilent data?

[Jianping Jin]

Hi Yong,

It is good to know that your files do have the Block column. I have never 
gotten that column in Agilent FT output files no matter of versions of 8.x. 
or 9.x as far as I can remember. I need to check with our core facility for 
that.

BTW Sean's suggestion worked well for me. Thanks a lot for your help!

JJ-

--On Tuesday, October 30, 2007 10:24 AM -0500 Yong Yin 
<yyin at watson.wustl.edu> wrote:

> 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 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
>
>
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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