[BioC] print layout for Agilent data?

[Jianping Jin]

Great Sean! You solved my problem.

Do you know an easy way to remove all Agilent control spots, including 
empty, negative and positive controls from a gene list to be analyzed.

best,

JJ-



--On Tuesday, October 30, 2007 10:54 AM -0400 Sean Davis 
<sdavis2 at mail.nih.gov> wrote:

> 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).
>
> Reading the help for normalizeWithinArrays, you might notice that the
> default method is "printtiploess".  That is fine, except that you need
> to specify the layout by hand.  However, Agilent does not use "print
> tips" or blocks, so printtiploess is not appropriate for Agilent arrays.
>  I think if you specify method="loess", you will probably find that
> things work just fine.
>
> Sean



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104, Campus
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at unc.edu