clusterProfiler
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YuLab-SMU
"No gene can be mapped" even with your own example
--> No gene can be mapped....
Hi,
I have tried to look for solutions for this in SO, biostars, bioconductor, your html manual, the PDF vignette, and your GitHub issues... nothing has worked, so here I am.
I want to use gseKEGG and enrichKEGG with Drosophila melanogaster differentially expressed genes, but I keep getting the error.
Probably the best minimal reproducible examples are from your online book/manual:
library(clusterProfiler)
geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05)
head(kk)
Reading KEGG annotation online: Reading KEGG annotation online: --> No gene can be mapped.... --> Expected input gene ID: --> return NULL...
kk2 <- gseKEGG(geneList = geneList,
organism = 'hsa',
minGSSize = 120,
pvalueCutoff = 0.05,
verbose = FALSE)
head(kk2)
Reading KEGG annotation online: Reading KEGG annotation online: --> No gene can be mapped.... --> Expected input gene ID: --> return NULL...
Things I have tried
(minimal example with Drosophila_genes)
# dummy data
df <- data.frame(gene_symbol = c("nAChRalpha2", "Act42A", "Ama", "ase", "asp", "Col4a1"),
ensemblGeneID = c("FBgn0000039", "FBgn0000043", "FBgn0000071", "FBgn0000137", "FBgn0000140", "FBgn0000299"),
log2FoldChange = c(-2.235647, -1.672559, -2.975020, -3.340225, -1.915317, -4.276045))
# to get the ncbi-geneid keys for each gene
ensembl <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL",
dataset="dmelanogaster_gene_ensembl",
host = "https://oct2022.archive.ensembl.org")
attributes <- listAttributes(ensembl)
ezlist <- getBM(attributes=c('entrezgene_id', 'ensembl_gene_id', 'external_gene_name'), mart = ensembl)
# get the NCBI gene IDs for the fly genes
df$`ncbi-geneid` <- ezlist %>%
filter(ensembl_gene_id %in% df$ensemblGeneID) %>%
dplyr::select(entrezgene_id) %>% unlist()
# try clusterProfiler KEGG tools
## (I have tried without as.character or as.list too)
kg <- enrichKEGG(gene = as.list(as.character(df$`ncbi-geneid`)),
organism = 'dme',
pvalueCutoff = 0.05)
--> No gene can be mapped.... --> Expected input gene ID: --> return NULL...
(note that this time it does no display "Reading KEGG annotation online:" ¯_(ツ)_/¯ )
I have checked directly that the annotations for my genes actually exist in the KEGG database:
# download the Drosophila KEGG keys versus NCBI gene IDs:
## (I got here inspecting your R code)
kegconv <- read.csv('https://rest.kegg.jp/conv/ncbi-geneid/dme/', sep = '\t', header = FALSE)
kegconv <- kegconv %>%
dplyr::rename(dme = V1, geneid = V2) %>%
mutate(dme = str_replace(dme, "dme:", ""),
geneid = str_replace(geneid, "ncbi-geneid:", ""))
# get the KEGG keys for my genes:
df$`kegg` <- kegconv %>%
filter(geneid %in% df$`ncbi-geneid`) %>%
dplyr::select(dme) %>% unlist()
# try clusterProfiler KEGG tools:
## (I have tried without as.list too)
kg2 <- enrichKEGG(gene = as.list(df$kegg),
organism = 'dme',
pvalueCutoff = 0.05)
All with with the same non-result. I am at my wits' end and I am no longer sure whether this is a problem with my code or an issue with yours or the KEGG API - that is why I am raising it here (as not even your example code in a clean session works for me).
I hope this is a real problem and not a silly mistake on my part, but I would be very grateful if you could suggest anything to make it work.
Could this have to do with the recent (minor) change in the KEGG API ? https://www.kegg.jp/kegg/rest/
I have also tried to do GSEA of KEGG pathways using other packages (gage) and I also run into trouble.
Could this have to do with the recent (minor) change in the KEGG API ? https://www.kegg.jp/kegg/rest/
I have also tried to do GSEA of KEGG pathways using other packages (gage) and I also run into trouble.
There is no changed any API syntax documents of KEGG. I fixed with updating clusterProfiler to 4.7 from 4.6. Hope this will help.
This is my session info.
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS/LAPACK: /home/fkt/mambaforge/envs/scRNA/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=ko_KR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=ko_KR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=ko_KR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] clusterProfiler_4.7.1.003 EnhancedVolcano_1.16.0
[3] ggrepel_0.9.3 ggpubr_0.6.0
[5] enrichplot_1.18.4 msigdbr_7.5.1
[7] org.Mm.eg.db_3.16.0 AnnotationDbi_1.60.2
[9] IRanges_2.32.0 S4Vectors_0.36.2
[11] Biobase_2.58.0 BiocGenerics_0.44.0
[13] future_1.31.0 forcats_1.0.0
[15] stringr_1.5.0 dplyr_1.1.2
[17] purrr_1.0.1 readr_2.1.4
[19] tidyr_1.3.0 tibble_3.2.1
[21] ggplot2_3.4.2 tidyverse_1.3.2
[23] SeuratObject_4.1.3 Seurat_4.3.0
Please use the latest version of clusterProfiler.
Hi, I also faced this problem. This version is "4.9.0".
ek <- enrichKEGG(gene = eg$ENTREZID, organism = "hsa", #人 pvalueCutoff =1, qvalueCutoff = 1, keyType = "ncbi-geneid") --> No gene can be mapped.... --> Expected input gene ID: --> return NULL...
I solved my problem. https://github.com/YuLab-SMU/clusterProfiler/issues/561#issuecomment-1467266614
Please use the latest version of clusterProfiler.
Hi, I've got same problem. And I use the latest version of clusterProfiler and I've tried this method(https://github.com/YuLab-SMU/clusterProfiler/issues/561#issuecomment-1467266614), but still show "No gene can be mapped". Hope you can help me to figure it out， thanks！
And this is my session info. ─ Session info ──────────────────────────────────────────────────────────────────── setting value version R version 4.3.0 (2023-04-21 ucrt) os Windows 10 x64 (build 19044) system x86_64, mingw32 ui RStudio language (EN) collate Chinese (Simplified)_China.utf8 ctype Chinese (Simplified)_China.utf8 tz Asia/Shanghai date 2023-06-09 rstudio 2023.03.1+446 Cherry Blossom (desktop) pandoc NA
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[1] C:/Users/61726/AppData/Local/R/win-library/4.3 [2] C:/Program Files/R/R-4.3.0/library
Hello,
I am having the same issue as the people above. Is there any timeline available for when will it be fixed, please?
Thank you
软件是好软件，安装是真难安装，富集也是出各种问题，为了装这个一个软件，重新安装R版本，将所有包重新装，结果还是不行。
难道真的不知道这个问题一直存在吗，难道只会微信宣传自己的人设，努力卖书？
好几年了，一直没有明确的解决方案，有问题不解决，无话可说。
祝好！
