ChIPSeeker Gene ID not matched error

Question

[Chenzhen Zhang]

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.

library('dplyr')
library("ChIPseeker")
library("org.Ce.eg.db")
library("TxDb.Celegans.UCSC.ce6.ensGene")
library("clusterProfiler")
txdb <- TxDb.Celegans.UCSC.ce6.ensGene

N2_K9_0.05<-readPeakFile("N2K9CallPeak_450_0.05_maxgap1000_peaks.broadPeak.bed")
peakAnno <- annotatePeak(N2_K9_0.05, tssRegion=c(-3000, 3000), 
                         TxDb=txdb, annoDb="org.Ce.eg.db")

I got this warning message:

Warning message:
In getGeneAnno(annoDb, peak.gr$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.

[backfish]

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