Nimblegen Expression Array With Limma

Question

[Raygozak]

Hi, does anyone knows how to get a set of .pair files for analysis with the lima package. i've seen some sort of answers, but they use examples from the biobase package and they don't make any sense or don't help much in importing this into an expression set.

Regards

Answer 1

[Neilfws]

There are a few suggestions in this thread on the Bioconductor mailing list. Two of them are (quoting from the replies):

1. "Get the NDF and XYS files from those who generated the pair files. Then use pdInfoBuilder as described in the vignette to create an annotation package. Later, you use the oligo pkg to read in the data and limma as you want."

2. "Another alternative: readNimblegen() in the 'Ringo' package returns an RGList object, which is limma-friendly."