For eNanoMapper, an EU project on nanomaterial safety I summarized the help pages and technical documentation of ArrayAnalysis.org and made these three tutorials. ArrayAnalysis.org is a free open source web tool for analysis of microarray transcriptomics data. The code is written in R and available at Github
How to use AffyQC module of ArrayAnalysis.org to do quality control and proprocessing on microarray raw data (.CEL files).
How to use the Statistics module of ArrayAnalysis.org to calculate fold change, log fold change, average expression, and significance on preprocessed (outcome of AffyQC tool) microarray data.
How to use the Pathway module of ArrayAnalysis.org to do pathway analysis.