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6.9 years ago
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I have a differntially expressed geneset. Some genes have an specific element in their promoters. I want to perform a hypergeometric test to see whether genes that have this element of their promoters are more likely to be differentially expressed than genes that do not have this element. I found that below one should be the relevent R function.
phyper(success-in-sample-1, success-in-bkgd, failure-in-bkgd, sample-size, lower.tail= FALSE);
What are the relevent parameters of my dataset. I can extract all the information from the dataset but dont understand what are they. For an example let's say I have 5000 differentially expressed genes. I found 4000 genes that have that element. So what are other parameters?
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?phyperin R will bring up the help information of that function.Thank you. I know that. But I dont know how to relate those paramters in my data set. For an example let's say I have 5000 differentially expressed genes. I found 4000 genes that have that element. So what are other parameters?
The other parameters to a hypergeometric test usually involve background. In other words, you have a set of all genes in your genome/universe ("background"). You measure how many of all genes have some characteristic of interest ("successes" in background). Then you have a subset of genes: genes of interest ("sample"). You measure how many of those have the same characteristic of interest (successes in sample). Those are your four parameters.
To add to that: the background are all the genes you could detect with your technology. For expression study that would be all genes which are expressed (optionally above a certain cutoff).