Differential Gene Expression Analysis with NimbleGen microarrays

Question

[pixie@bioinfo]

I am analyzing microarrays from the platform NimbleGen Arabidopsis thaliana 4x72K Array [080306_AT6_expr]

(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16226)

Is there any well-defined pipeline for its analysis to identify deferentially expressed genes using R package or any other tool ?

Kindly help.

Answer 1

[morovatunc]

You my check oligo R library for analysing Nimblegen data. It has quite well defined manual.

[pixie@bioinfo]

Thank You, the paper for the dataset I am using also uses oligo as well as pdInfoBuilder (Falcon et al., 2012) packages using the AgilentAT6 build. I was wondering why they have used the pdInfoBuilder package.

[morovatunc]

This is one of the most confusing things about that package. It creates such a "class" to annotate genes. For my case, I didn't have to chance to use annotation file that is downloaded from the database. Therefore, I had to create it manually. Hope your build is available online.