Green monkey edgeR in GSEA analysis
Hi everyone I'm looking forward to any method that could figure out the green monkey GSEA result. Here's my edgeR result without replicated
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gene_id logFC logCPM PValue
1 ENSCSAG00000017073 1.150721465 5.910470 0.32345174
2 ENSCSAG00000017066 0.582885576 6.407902 0.57298122
3 ENSCSAG00000017031 0.670118266 5.910375 0.62413986
4 ENSCSAG00000017027 -1.140139418 5.909995 0.32345174
How can I process to Because I didn't find any green monkey annotation package in bio-conductor
kk2 <- gseKEGG(geneList = geneList,
organism = geneList_organism,
nPerm = 10000,
minGSSize = 3,
maxGSSize = 800,
pvalueCutoff = 0.05,
pAdjustMethod = "none",
keyType = "ncbi-proteinid")
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figure out the green monkey GSEA resultmean exactly? I take it for granted that you know that any unreplicated results is neither reliable nor publishable.Hi ATpoint Because we know that R packages do not support any species of green monkey on Bio-conductor annotation. So how can I use those log fold change result attached on GSEA? And I also know this data can't be published, it just wants to know having any phenome inside that.
Your best chance is probably to try mapping the gene names of your species to the human orthologs. I am not familiar with your species so I cannot recommend any source for it, maybe Ensembl is worth a look, there are many threads here at Biostars on how to use biomaRt for the conversion. With the human orthologs you can then perform GSEA or any other kind of enrichment analysis to get an idea what is going on in your data.
OK, I took your advice and also got some interesting result, thx