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Thread: compare a non ranked list to a ranked list

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    compare a non ranked list to a ranked list




    Hi,
    I need to compare a small list of genes (genes of interests) to a big ranked list of genes (9000) where the 1st one is shown to have an effect and the last no effect.
    My small list is composed of metabolic genes ( so only one category) dissiminated in this big list of 9000 genes that are for some metabolic but you have others categories.
    My aim is to show that my tool finds the metabolic genes of interest, ( the ones which are situated more to the top of the list). Is there way to do so without setting a treshold ?
    Thank you

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    Re: compare a non ranked list to a ranked list

    I'm not 100% sure I understand your question fully. It sounds to me that you want to show that the small list of genes contains more genes that are in the top of the big list than in the bottom.

    Maybe, then, it would be interesting to partition your big list into quantiles (e.g. 10 quantiles of 900 genes each), with quantile 1 containing the top ranked genes, and quantile 10 containing the lowest ranked genes. You can then test how big a proportion of genes in each quantile is in your small list, and test these proportions for significance using a Fisher's exact test.

    Ideally, the outcome would be that the proportion decreases with quantile number, meaning you find more genes in the top of the ranked list than in the bottom.

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  4. #3
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    Re: compare a non ranked list to a ranked list


    Hi, Thank you. You got it right . That's exactly what I want to do. In others therms: how do you prove that the smallest list is not equally distributed across the big list. I'm really glad to get a reply.

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