DEG analysis of microarray data using R (.cel file unavailable)

Question

[sunifeb12]

I would like to do a differential gene expression analysis on a microarray data using the simpleaffy package in R. I was following this particular tutorial for doing the analysis, as I am a newbie in this field. Unfortunately, for a particular dataset used for my study, .cel file is not available and only .txt file/ SOFT file is available for download. Can these files be analysed using the simpleaffy package? Or is there a way out how to proceed with the analysis? Any help in this would be greatly appreciated.

Thanks!

Answer 1

[h.mon]

You can use the GEOquery package, see this tutorial for help:

https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/

[sunifeb12]

So after loading the SOFT file to R using GEOquery, would I be able to proceed with the pre-processing & analysis using the simpleaffy package? Thanks for the suggestion!