Question: Nimblegen Expression Array With Limma
1
gravatar for Raygozak
6.9 years ago by
Raygozak1.3k
State College, PA, Penn State
Raygozak1.3k wrote:

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

R bioconductor microarray • 1.9k views
ADD COMMENTlink written 6.9 years ago by Raygozak1.3k
3
gravatar for Neilfws
6.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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."

ADD COMMENTlink written 6.9 years ago by Neilfws48k
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