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Question: Properly assigning gene list objects in GOsummaries
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gravatar for Bohdan Khomtchouk
3 months ago by
Stanford University
Bohdan Khomtchouk10 wrote:

I'd like to use the GOsummaries package in a workflow that I'm building.  But I do not understand the rationale behind how the genes1 and genes2 vectors were constructed in the package vignette (page 2): https://bioconductor.org/packages/release/bioc/vignettes/GOsummaries/inst/doc/GOsummaries-basics.pdf.  I have a gene list like mygenes = c("some_gene1", "some_gene2", ... "some_geneN") that I'd like to use the GOsummaries package with.  Do I need to assign my gene list to one object (e.g., genes1) and then assign the entire genome gene list to another object (e.g., genes2) and then do gl = list(List = list(genes1, genes2)) or is there some other way?

 

 

ADD COMMENTlink modified 3 months ago by Raivo Kolde50 • written 3 months ago by Bohdan Khomtchouk10
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gravatar for Raivo Kolde
3 months ago by
Raivo Kolde50
Boston
Raivo Kolde50 wrote:

If you have the mygenes variable that is a gene name vector already, then just enter gl = list(MyGeneList = mygenesand you should be good.

ADD COMMENTlink written 3 months ago by Raivo Kolde50

This is the error I now get:

P.S.  Doesn't one need to also specify the organism prior to generating a word cloud (i.e., for the apriori GO enrichment analysis)?  Here, my gene list has an RGD entry, so is clearly rat, but how would the GOsummaries package know what organism you're working with ahead of time?  Thanks for clarifying.

ADD REPLYlink modified 3 months ago • written 3 months ago by Bohdan Khomtchouk10
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