Fisher test in R to compare percentages of three databases
Entering edit mode
10 months ago

Hello everyone!

So sorry if this is a very basic question for you, but I am fairly new to both bioinformatics and statistics. I have a 4x15 dataframe with genes and percentage of mutation for every gene in three databases, just like this:

Gene    UdeI    MSK TCGA
TP53     46  74  53
KRAS     31  51  43
PIK3CA   23  19  15

and need to compare if there is a significant difference between the first database (UdeI) and the others two, so I thought that a Fisher test was the most appropriate statistical test to do this, so I would like to know how can I do it using R. I will really appreciate any help you can give me, Thanks in advance

test fisher R statistics • 310 views
Entering edit mode

Fisher test only tests 2x2 tables =) you need some form of ANOVA here, but moreover, you need to transform percentages into actual counts (in other words, you must know the sample size)


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