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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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difference between online and local GREAT analysis #46

Closed wbvguo closed 5 months ago

wbvguo commented 8 months ago

Dear rGREAT developer,

I recently tried the tool for online and local analysis using the following code:

job_online = submitGreatJob(gr = region, bg = bg_region, species = "hg38", rule = "twoClosest")
job_local_gobp = great(gr = region, background = bg_region, gene_sets = "GO:BP", tss_source = "GREAT:hg38",  mode = "twoClosest")

Although we used the same regions and background regions in these 2 analyses, the BP enrichment results in job_online is quite different from the job_local_gobp result. I am interested in what factors caused the major difference. In addition to the annotation version difference, would it be because the rGREAT local algorithm is quite different from that of the GREAT original algorithm?

Thanks,

jokergoo commented 7 months ago

Hi Wenbin,

Sorry for the late reply. Unfortunately, I am very busy with other things.

Maybe you can check these documents: https://jokergoo.github.io/rGREAT/articles/other-docs.html

One possible reason is the GO data on the GREAT website is very old. The algorithm should be the same.

wbvguo commented 7 months ago

Got it! totally understood, no worries at all.

Thanks for the replies, I will check the documents first.

Best,