To all users of limma,

 

We are using limma package for differential gene expression analysis. We also use weights (0 and 1) based on quality control from image analysis. We know that spots with weight 0 are not included into normalisation of data (although the MA values are calculated for them also - as explained in Limma User's Guide). Our question is what happens with these "0-weight" spots during further DE analysis in limma package?

 

Is there any chance that they might appear in the toptable? What to do in that case (simply ignore them)? Or do you suggest filtering them out after normalisation?

 

 

Matjaz and Spela

 

 

National Institute of Biology, Ljubljana, Slovenia


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