I came across a problem when I did GO analysis on differentially expressed genes derived from microarray using clusterProfiler . I gave a list of DEGs but failed to map any gene with the enrichGO() function.
I used the following script to do the analysis:
gene <- names(geneList)
ego <- enrichGO(gene = gene,
universe = names(geneList),
OrgDb = org.Mm.eg.db,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.1,
minGSSize = 3,
maxGSSize = 500
Unfortunately, an error message was returned saying
--> No gene can be mapped....
--> Expected input gene ID: 442829,71950,100041897,71711,11535,19264
--> return NULL...
I obtained the data as input of enrichGO() from differentially expressed genes of microarray data using limma.
However, I got the GO enrichment result with “PANTHER” an online GO analysis tool.
I even loaded the entrez gene id from a txt file (as shown in attachment) but got the same error. The code to load the data was “genes <- read.csv("genes.txt", header = FALSE)“.
Could anyone help solve this problem?
Thanks in advance!