Finding differentially expressed genes in Control vs. Treated

Question

[Bioinformatist Newbie]

I have 2 .cell files containing gene expression data for Control and Treated cell lines (downloaded from GEO). I want to find differentially expressed genes in them. Can anyone share some nice step by step guide to do this task. I have tried this tutorial but ended up in following error while filtering my data:

(celfiles.filtered <- nsFilter(celfiles.gcrma, require.entrez=FALSE, remove.dupEntrez=FALSE):

Error in rowQ(eSet, floor(0.25 * numSamp)) :
  cannot calculate order statistic on object with 2 columns

Thanks

[Devon Ryan]

You can't hope to get much out of a 1 vs. 1 comparison.

[alolex]

It looks like you are getting that error because you do not have any replicates. Does the GEO dataset you are using have replicates? As commented already, you won't get anything useful if you don't have replicates for each condition.

Answer 1

[andrew]

Agreed with the above answers. We have an application that lets the user submit raw .cel files for differential expression analysis (including QC and normalization) for free and we require a minimum of 3 samples per group (3 condition vs. 3 control). If you want to try it, you can access the application at http://www.ipathwayguide.com