[BioC] Quality checks / flagging
Yves.Bastide at irisa.fr
Thu Sep 18 10:04:55 MEST 2003
Gordon Smyth wrote:
> 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
> 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.
An even more elementary question (disclaimer: I am not a statistician):
how to use these weights to make limma ignore some lines? I naively
tried with weights of 0 and 1, but it didn't work as expected.
> 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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