data pre-proccessing and matrix building in R

Question

[zizigolu]

Hey friends,

I have a micro array experiment, I am going to pre-process it using the MAS 5.0 algorithm and align to build a matrix in the 'R' then Probe sets that were found 'absent' on ≥ 10 % of microarray chip to will be omitted from further analysis (i don't know how do this also). I installed R....

Right now after hours searching, I got fully puzzled, please don't leave me alone in this step

Thanks

[SES]

You will need to provide more information and ask a specific question if you want some help. Show some data and where you are getting stuck with a specific command or problem.

Answer 1

[Sean Davis]

Well, if you are going to do this in R and you have not used R before, you'll likely need to do a little learning online. Then, you can pick up with Bioconductor and perhaps start with this page for affymetrix oligo arrays.

http://bioconductor.org/help/workflows/arrays/

If or when you get stuck, you can write back with more specific questions.

[zizigolu]

Thanks a lot

Answer 2

[poisonAlien]

Here .. Try this tutorial. They explain how to use mas5 to remove absent probes.