How do I make a graph displaying "# of Genes" vs. "Expression Lev - (Jul/29/2008 )
I've done a few microarray experiments in the past, and I love using dChip for my data mining. However, I got a request from my advisor to create a particular type of graph. On the x-axis, she'd like to see a range of normalized expression levels (from 0 to, say, 5000 in 10 unit stretches). And on the y-axis, a tally of the number of genes that were found in each expression level range.
It'd be a global look at each chip, with the peaks towards the lower end, most likely.
The problem - and my question - is what program can spit this out? I'm sure there's a way to do it in Excel, even, but I have no idea how you'd make a tally of genes from the raw values like that.
I haven't checked the finer points of GeneSpring or GeneSifter, but has anybody seen a graph like this with microarray data?
You're describing a histogram. Excel can do them; see here for example. If you don't have the Data Analysis Tool pak installed in Excel, there are other way to do it -- Google "Excel histograms".
Whoops, I was overlooking that term. I'm a moron. I was manually making COUNTIF() descriptors to do it in Excel before I gave up and came here.
do you know WinStat? It is a tool that is implemented into excel after installation and very easy to use. Additionally, it provides different layouts of histograms and many more statistical applications. A demo version available for 30 days. In my opinion, the histogram "tool" of excel is not very useful, but maybe in the newest versions of excel it is more advantageous.
A bit harsh, don't you think? We all have brain freezes; sometimes my brain unfreezes when I'm typing a post -- in trying to explain what I'm asking, I explain it to myself...!
Anyway, hope it helped, and welcome to the forums!