[BioC] print layout for Agilent data?

[Sean Davis]

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