This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Help: how to use wilcox.test with a SummarizedExperiment object?

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!

summarizedexperiment wilcox.test
• 809 views • link
written by longsong • longsong

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.

• 0 views • link
written by shawn.w.foley shawn.w.foley

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.

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this