Question: (Closed) Help: how to use wilcox.test with a SummarizedExperiment object?
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gravatar for longsong
10 months ago by
longsong0
longsong0 wrote:

I have a SummarizedExperiment object (not RangedSummarizedExperiment object): se.

The row names are Gene IDs, and columns names are sample names. Samples are divided into 2 groups: A and V groups. The ‘Column’ (sample) data has a filed: group, which has the values of A or V.

The object has only one assay, which is a integer count.

Now I'd like to use Wilcoxon-Mann-Whitney test to check: for each Gene ID, for A group and V group, the count is different or not?

It maybe a simple question, but I am still a learner of Bioconductor and not know how to do it.

Anyone can help me?

Thanks!

ADD COMMENTlink written 10 months ago by longsong0

Could you post a few example lines of your file? I'm not quite sure what you're asking for, do you want a p-value for each gene comparing A vs V, or do you want a single p-value comparing all genes in A versus all genes in V? If it's the first option it sounds like this is an n=1 experiment, in which case you cannot generate a p-value.

It'd be great to have some more context too. Is this RNA-seq? Microarray? How are you processing the data to generate a SummarizedExperiment object? More information will let the community better help you.

ADD REPLYlink written 10 months ago by shawn.w.foley1.2k

It would be also helpful to know (given this is normal NGS data like RNA-seq) why you do custom statistics rather than using established tools like DESeq2/edgeR/limmafor it.

ADD REPLYlink written 10 months ago by ATpoint31k

Hello longsong!

Closed due to having been cross-posted: https://support.bioconductor.org/p/121358/

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 10 months ago • written 10 months ago by Kevin Blighe56k
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