[BioC] Quality checks / flagging
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
>>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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