Question: DEG analysis of microarray data using R (.cel file unavailable)
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gravatar for sunifeb12
17 months ago by
sunifeb120
sunifeb120 wrote:

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!

ADD COMMENTlink modified 17 months ago by h.mon27k • written 17 months ago by sunifeb120
0
gravatar for h.mon
17 months ago by
h.mon27k
Brazil
h.mon27k wrote:

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

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

ADD COMMENTlink written 17 months ago by h.mon27k

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!

ADD REPLYlink written 17 months ago by sunifeb120
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