[BioC] Quality checks / flagging

[Gordon Smyth]

See function read.maimages() and the section QualityWeights in the limma 
package. You can read in any weight functions or flags that you can 
calculate from the GenePix files, i.e.,

   RG <- read.maimages(files,source="genepix",wtfun=myweightfun)

where myweightfun is any function which you have defined which takes 
Genepix data from one array as a matrix or data.frame and computes from it 
a column of flags or quality weights. These weights then become part of the 
component

   RG$weights

Note that read.maimages() produces an RGList object which is essentially 
equivalent to a marrayRaw object. You can transform it to an marrayRaw 
object if you want.

Gordon

At 11:22 AM 18/09/2003, Tan, MinHan wrote:
>Hi,
>
>Sorry - this sounds like a rather elementary question - but is there any
>way I can read in selected columns into the marrayRaw object using
>read.genepix? (e.g. % > B532+2SD)
>
>Instead of performing quality flagging in GenePix, I was wondering how
>to achieve the same thing in R.
>
>Thank you!
>
>Regards,
>Min-Han