fisher test on row

Question

[yasjas]

                     tissu1       tissu 2              total in genome
(A)n                 92           89                   13606
(AAATG)n             0            1                    372
(AACTG)n             0            0                    11
(AAGTG)n             0            0                    21
(AATAG)n             1            1                    159
(AATTG)n             1            0                    96

I have a question on how to make a fisher test to see if some the elements are more present in tissu 1 than 2 I couldn't manage to do it for each row.any help please?

Answer 1

[mehran.karimzade]

For a Fisher's exact test you have to create a contingency table with two rows and two columns.

Column names: Proteins existing in tissue 1, Proteins not existing in tissue 1

Row names: Proteins existing in tissue 2, Proteins not existing in tissue 2

If this table means that there is no shared protein between tissue 1 and tissue 2, then in R you can do:

mat$Fisher.Pvalue = apply(mat,1,function(x){return(fisher.test(matrix(c(0,x[2],x[1],x[3]-x[2]-x[1]),nrow=2))[[1]])})

[Devon Ryan]

I assume you mean:

apply(mat, 1, function(x) fisher.test(rbind(x[1:2],x[3]-x[1:2]))$p.value)