Is it possible to use limma to simultaneously analyze RNA-seq and gene expression array data?

Question

[njbernstein]

I have two datasets with cases and controls for the same disease. One dataset has bulk RNA-seq data and one dataset was measured using an affy gene expression array. Is it possible to analyze these at the same time using limma, e.g. ~ disease_state + affy_or_rna_seq? or is it best to analyze each individually and then meta-analyze the results?

Gordon Smyth any thoughts here?

Answer 1

[Gordon Smyth]

Definitely best to analyse separately and to relate the two analyses using gene set tests etc.

The technologies can't be analysed as one data set because they have different feature sets, different precisions and differerent mean-variance relationships.

[njbernstein]

Sounds good. Thanks!