Question

Can I use compareCluster function to compare genes upregulated in various clusters of cells?

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charlesgwellem ▴ 10

@charlesgwellem-16293

Last seen 2.8 years ago

Germany

Hi, I have a group of genes upregulated in various clusters of cells when I run Seurat's FindAllMarkers() function. Is it statistically correct to use run compareCluster::compareCluster() on a list of these upregulated genes grouped per cell cluster? Or must the genes be grouped per GO before running compareCluster().

Thanks in advance for your kind help.

clusterProfiler bioconductor • 1.9k views

ADD COMMENT • link updated 4.6 years ago by James W. MacDonald 67k • written 4.6 years ago by charlesgwellem ▴ 10

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Not sure whether I am answering your question, but the function compareCluster() will automagically check whether the input genes have a GO annotation (through the annotation info in org.Hs.eg.db (when working with human genes)). Those genes that don't have a GO annotation will be discarded from the analysis. Then a (simple) over-representation analysis will be performed for each cluster (=set of selected genes).

ADD REPLY • link 4.6 years ago Guido Hooiveld ★ 4.1k

score 0 · Answer 1 · 2020-07-08

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 15 hours ago

United States

Seurat isn't a Bioconductor package, so your question is off-topic for this site. You can evidently post questions on their github page.

ADD COMMENT • link 4.6 years ago James W. MacDonald 67k

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I think OP means the compareCluster function in the Bioconductor clusterProfiler package.

ADD REPLY • link 4.6 years ago Gordon Smyth 52k