My data is from affymetrix Genechip Human Gene 1.0 ST Array that I want perform a gene differential expression analysis on. The data consists of two different tissue samples. I have access to the raw data containg 12 .CEL files. 

What package should I use and how do I analyse the data to find  genes that are differently expressed between two tissue samples? 

Thanks.

Dear Dave,

check the following post:

C: Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotati

It is for Gene ST 2.0 arrays but the basic pipeline is the same.

Moreover, you should definately check and read limma R package users guide, for comprehensive analysis and statistical testing of many types of gene expression data:

http://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf

Also, you can check the vignette of the package oligo (mainly for import and basic preprocess of Gene ST arrays):

http://bioconductor.org/packages/release/bioc/html/oligo.html

& the relative workflows of bioconductor available:

http://www.bioconductor.org/help/workflows/arrays/

Best,

Efstathios