The last weeks I spent on the processing of transcriptomics data of my cell culture experiments. Between the gene and the protein there is a level, where we can see the products of gene transcription. The abundance of transcripts in biological samples was determined by a microarray in which 36,000 transcripts are analyzed at once. The output we then get are huge excel files which contain thousands of genes and values. At this point the big challenge is to find the correct way to analyze and interpret them - in other words: find the needle in a very big haystack.
Before I could start with my hunt for the needle, I had to learn a completely new and different way of lab-work... data processing, correction, statistical analysis for multiple testing... everything very different from the lab-work I was used to do.
After months and months of cell culture work, hundreds of RNA extractions, sample pre-processing and months of waiting until our samples are finally analyzed, processing steps and statistical analysis for over expressed genes and biological pathways I'm still not finished... now the obtained data require interpretation - in other words: now that I found a couple of needles... what does it mean?