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_posts/2007-07-12-full-speed-ahead.markdown

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+---
+author: einar
+comments: true
+date: 2007-07-12 19:20:55+00:00
+layout: post
+slug: full-speed-ahead
+title: Full speed ahead
+wordpress_id: 271
+categories:
+- Science
+---
+
+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](http://www-stat.stanford.edu/~tibs/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](http://bioconductor.org/packages/2.0/bioc/html/siggenes.html) 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...