Analysing microarray data

Question

[haqshenas]

Hi, I am new in this field. I am trying to extract RNA microarray results from a published paper. I have extracted the data from the EBI website. The ID is E-GEOD-20948. I need help to analyse the data after I download them in cel format. I am currently stuck in the first step that is opening the files. Any program opens this format. I have tried GIMP-2 and quicktime but no success. I appreciate your help. Reza

[venu]

Did you check this one

Analysing Microarray Data In Bioconductor

[zizigolu]

Hi Reza, go http://mapman.gabipd.org/web/guest/robin download and install RobiNA then upload your CEL files and run the program. extract RNA microarray results will be in results folder. movafaq bashi

[haqshenas]

Thanks for your reply. For some reason it is not installed correctly. At the last step when I click on "Next" it goes forever.

Answer 1

[newbiebio]

You could read the link that Venu recommanded or click this link(http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html)

Usually, we use affy and limma package from Bioconductor to analysis microarray data. source("https://bioconductor.org/biocLite.R")

download these two packages

biocLite("affy")

biocLite("limma")

load these two libraries

library(affy)

library(limma)

use ReadAffy function of the affy package to read the CEL files

data=ReadAffy() #you could check the links that we provided for more information