[BioC] Quality checks / flagging

Gordon Smyth smyth at wehi.edu.au
Thu Sep 18 12:51:20 MEST 2003

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 


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.


At 11:22 AM 18/09/2003, Tan, MinHan wrote:
>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!

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