Entering edit mode
7.5 years ago
fatemehnorouzi47
•
0
hi , I have several RNAseq experiments in a project . In the step of filtering , in one experiment t-test gives appropriate number of genes , in another one, Beggerly test gives suitable number of genes and t-test doesn't answer . It makes me confused . Is it possible that in a project we use different types of statistical analysis in its different experiments? my experiments have repetition . thanks,
What are you testing with t-tests and beggerly tests? What do you aim to achieve and how are you running the tests?
Dear Fatemeh, Hi
Are you intend to perform some DEG analysis? it is not clear that what is the purpose of using t-test. are you comparing for example the FPKM of some candidate gene in this way (which I guess it is not a correct approach)?
Dear Farbod,
I don't intend to compare the FPKM, I have some experiments for treatment case and some for control case, differential expression genes are manifold , I want to reduce them , I am filtering with Fold change and Pvalue , there are three types of Pvalue according to three test that I run on my data,(I mean t-test,DEG,Baggerley test).Now I want to choose among them .
Have you tried FDR as a filtering threshold?
By the way, I do not get the point why you are trying to reduce your DEGs?
Are you already know the answer of your investigation ?
~ Take care
Do you mean "Baggerly's test" (i.e., this)? I thought that was essentially a beta-binomial, which wouldn't normally be appropriate (the distribution is annoying to fit properly to begin with).
Dear Devon, thanks for your reply , I couldn't find this, Is it possible to compare these three tests( Baggerley , t-test , DEG) with each other? I need a brief explanation about them.
thanks
I assume that you're using CLC. If so, call them and ask them to give you a short writeup on this. You're paying them already, so they'll tell you what you need to know.
Also, I don't know what "DEG" would be in this context. Normally that's "differentially expressed genes", but that's not any particular test.