5.3 Extracting specific measurements
To make up for their practical joke earlier, our statistician friends have now come back and provided us with a list of the one hundred genes that their analysis tells them are most important in differentiating between the \(ALL\) and \(AML\) groups in our experiment. They have also admitted that there weren’t really any outliers after all. To study these further, we therefore want to retrieve the log transformed and normalised intensity values of just these one hundred probes for all 38 of our original samples.
- Read in the list of 100 probe IDs and associated gene names from the data file “golub100.txt”
Hint: the gene names are in column 2 of this tab-delimited file, the probe IDs in column 1
- Generate a new matrix of log normalised values for all 38 samples and the 100 genes in this list
We will now try further practice on an alternative input dataset. Before doing this, it would again be worth saving your R workspace and your markdown code. Perhaps open a new markdown document for this second dataset