[BioC] Quality checks / flagging

[Yves Bastide]

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
> 
>   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
> 

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.

Regards,

yves


> 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
> 
> 
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