Question: ChIPSeeker Gene ID not matched error
gravatar for Chenzhen Zhang
16 months ago by
Rutgers University
Chenzhen Zhang10 wrote:

Hi I am using the ChIPSeeker package to do gene annotation for ChIP-seq data. broadpeak files were generated with MACS2. Here is my code.

txdb <- TxDb.Celegans.UCSC.ce6.ensGene

peakAnno <- annotatePeak(N2_K9_0.05, tssRegion=c(-3000, 3000), 
                         TxDb=txdb, annoDb="")

I got this warning message:

Warning message:
In getGeneAnno(annoDb,$geneId, type) :
  ID type not matched, gene annotation will not be added...

HELP! How can I match the ID type? I checked the txdb and and annoDb files, both of which have Ensembl gene ID.

chip-seq chipseeker • 609 views
ADD COMMENTlink modified 8 hours ago by floriandeckert0 • written 16 months ago by Chenzhen Zhang10

Hi Zhang,

I have the same problem. What is your R and ChIPseeker version? In my case its R 3.6.1 but ChIPseeker is 1.22.1 (which is very old and I can't update).

Hence, there might be a confusion with the org and TxDb due to old ChIPseeker version.

Best, and thanks, Florian

ADD REPLYlink written 8 hours ago by floriandeckert0
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