[BioC] print layout for Agilent data?

[Sean Davis]

Jianping Jin wrote:
> 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.

I believe the controltype column contains these information.  You can
just remove probes with controltype!=0, if I recall correctly.


> --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