fisher exact test

Question

[Edalat]

hello everyone,

I want to determine p-value for lncRNA according to Fisher’s exact test,but I cannot understand what should I do?which parameter should I use?

(I have some differential expression gene of some experiments for lncRNA)

anyone can help me?

I read the article of (Identification of long non-coding RNAs involved in neuronal development and intellectual disability) "doi:10.1038/srep28396 " which use this test for determine p-value.

Answer 1

[Sean Davis]

I would suggest adopting a more standard approach such as edgeR, DESeq2, or limma voom. All of these are available from Bioconductor, are well-supported, have good documentation, and represent state-of-the-art approaches to testing for differential expression in RNA-seq. If you have something other than RNA-seq as your input data, please update your question with details.

[Edalat]

thank you for a reply.No, I have only RNAseq

[WouterDeCoster]

Then this guide (and many other) might be of interest: http://www.bioconductor.org/help/workflows/rnaseqGene/