I have extracted DNA and RNA from the same set of sample (Tumor and normal biopsy) and used them to run Cytoscan HD and Exon arrays. Now we want to do patient wise analysis for cytogenetic events as well as gene expression. We have only one array for each patient, so no technical replicates. We don't want to group all tumors into one and normal into another in order to capture patient specific unique events.
you can import the data (individual array files) into R, merge the data files based on the identification of the gene/probeset. usually each array is a column and gene/probset is a row to create a matrix. you may have to load the phenotype file containing the patient information containing the array id separately though. once the dataset is read and phenotype information linked. then rest is simple steps:
1. check the quality of your data
2. clean up the data
3. if required normalize the data accross all the arrays
4. design a comparison matrix to do the analysis
if you have a background in statistics then not a problem, otherwise you are better off with a statistician.
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