[BioC] Quality checks / flagging

Gordon Smyth smyth at wehi.edu.au
Thu Sep 18 18:16:40 MEST 2003

At 05:04 PM 18/09/2003, Yves Bastide wrote:
>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.
>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.

Weights of 0 and 1 do have the effect of ignoring the log-ratios for spots 
with zero weight. I am not sure what you mean by "ignore some lines". 
Please explain further what you did and what you expected to happen which 



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