Hello,

I have been searching to find a method to define up or down regulated of a set of genes. There are plenty of R packages in Bioconductor. Note that I cannot use any because I only have one matrix. I don't have any reference matrix nor do I have phynotype etc.

Is there any package which allow me to define up or down regulated of my genes ?

Thanks  

Up- and down-regulated genes are always defined relatively between two groups of samples.  This is why there are no packages to do such an analysis.  You'll need to come up with one or more questions that you can answer with your data, perhaps starting with some unsupervised analyses (clustering, MDS, etc.).  That said, if you truly know nothing about the samples, then the task of finding important information in your data is that much harder.

@ Sean Davis, what about GSEA? do you think it is possible to perform such analysis ?