How to use ClusterProfiler

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14 months ago

ochiengwycliffe5 • 0

Hello,

I have been trying to analyze and visualize data using clusterprofiler but still get this error. Is there anyone who has encountered the same problem ? and how did you go about it? Thank you enter image description here

ClusterProfiler • 1.0k views

ADD COMMENT • link 14 months ago by ochiengwycliffe5 • 0

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This is an example of my gene symbol;

"11S2_SESIN" , "11SB_CUCMA", "1433_LILLO" , "AAT5_ARATH"

ADD REPLY • link updated 14 months ago by Ram 43k • written 14 months ago by ochiengwycliffe5 • 0

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What is this? It's for sure not HGNC gene symbols. How was it obtained?

ADD REPLY • link 14 months ago by ATpoint 81k

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They look like sequencing names from UniProtKB Swiss-Prot/TrEMBL. I am not familiar with them, but you definitely need to convert to geneSymbol (maybe after collapsing the entries from the same organisms together??).

ADD REPLY • link 14 months ago by fracarb8 ★ 1.6k

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Yes, they are BLASTX_Sprot_TopHit obtained from an annotation file. I used them because they were easier to run in RASFlow compared to the transcripts i.e transcript24381_f2p60_1851.

ADD REPLY • link 14 months ago by ochiengwycliffe5 • 0

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Looks like these are gene ID/symbols from plants so you can't use human gene annotation.