This TP is a practice exam. For the following data set, you should carry out a comprehensive data analysis, including exploration, quality assessment, quantification of expression, identification of differentially expressed genes and a cluster analysis (cluster the samples to see if there are unknown subgroups, not the genes), and write a report summarizing your findings.
This experiment was carried out with Affymetrix GeneChips to determine differences in gene expression between placenta and testis. You can download the data from http://lausanne.isb-sib.ch/~darlene/gda/PT.zip.
You have two jobs here:
I will not give a lot of instruction here, you should have the pieces already from the previous TPs. Hint: the limma User's Guide might be very useful.
I will mark your report according to the criteria in the file below (see also the additional exam guidelines file), taking into account: overall presentation, statement of background and objectives, summary of quality assessment (including supporting graphs), description of statistical analyses carried out (including description of any models fitted, design matrix, contrasts if necessary, etc.), (apparent) correctness of results (including some kind of table giving genes that are differentially expressed, along with the top 50 genes in any case), cluster analysis and conclusions. As an appendix, you should also include a separate plain text (ASCII) file with clean R code so that I will be able to replicate the results you present.
I expect this TP to take longer than the previous ones, so you will also have time to work on it in the following weeks.
As usual, your report can be in English or French.
Please send your report as a pdf file, and follow the naming convention:
surname7.pdf for the report, surname7.R or surname7.Rnw/surname.Snw or surname.Rmd
(plain text file) for the R code
(e.g. my files would be goldstein7.pdf and goldstein7.Rnw or goldstein.Rmd).
If you email your report to me
Feel free to ask/email me if you have any questions. Have fun and GOOD LUCK!!