Hello, I am looking for some advice. I have 18 diseased tissue's, 11 normal and 21 DE genes. I want to find the best predictors of disease using these genes. If anyone has any experience of predictive models, I would be interested in the processes and any caveats and also some useful visualization tips would be welcome.
1 answer
Hey Marion,
It can be as simple as creating a combined regression model of the form Disease ~ gene1 + gene2 + ... + gene21 and then deriving test statistics from this, such as AUC, sensitivity, specificity, accuracy, and precision. You will likely reduce this model further —either manually by checking term (gene) p-values, or via other procedures like stepwise regression— as some genes may offer minimal information.
There is a lot of material online, but perhaps no 'all encompassing' tutorial. I have posted various answers that may be of interest to you:
- A: Resources for gene signature creation
- A: How to exclude some of breast cancer subtypes just by looking at gene expressio
- A: What is the best way to combine machine learning algorithms for feature selectio
Any specific questions, please do ask.
Kevin
Log in to answer this question.
Thank you so Kevin much for that information, its a great suggestion and more specific to what I am trying to achieve. I was getting very bogged down in the amount of information and tools out there as my data set is very simple, glad I asked.
Thanks again Marion
No problem