[BioC] QualityWeights (using limma)

[Gordon Smyth]

At 01:35 AM 17/03/2004, joycel_balaena.bio.vu.nl wrote:
>I am using the limma application and am wondering whether there are is a
>QualityWeights function available for Imagene? If not, is there an 
>alternative
>way to compute QualityWeights when using data from the Imagene image analysis
>program?

We work with Imagene data very seldom and so have not developed our own 
weighting scheme for Imagene data. Since Image output comes with a 'Flag' 
column, the best I can suggest is that you can simply convert the flags to 
numeric weights, i.e.,

    wt.fun=function(x) as.numeric(x$Flag==0)

Does anyone who works with Imagene have a better suggestion?

Gordon

>Hope someone can help me out,
>Joyce van de Leemput