Full speed ahead

After giving in the summary of my thesis today, I also started writing the actual thing. Of course this is not something I will finish in a few days. It’s a long journey that will go on until I deliver it.

Aside that, I’ve been having some problems with R, a language which I really don’t like and I hope to use as less as possible. I was obtaining a list of  differentially expressed genes (DEGs) out of some data files with SAM, and of course I had to supply a matrix with expression values for every gene.

What I didn’t understand is why on Earth the package siggenes understands that, but when outputting the result (command sam2excel) it’s giving the  row of the file where the gene is, instead of the actual gene. If I supplied the IDs, whatever they are, they should be added as well!  But you can output those only with “list.siggenes” which of course doesn’t add the d-score I need…

In general, I find R slow, clumsy and counter-intuitive. There are much better languages out there (and with better interactive shells), I can’t really understand why it is so popular among people who do bioinformatics…