I am a student currenty trying to learn how to use clusterProfiler. I figured out a few things but I still have many issues, (I apologize, I know that usually its' better to ask only one question), since I also have a lack of knowledge in this field of biology.
First, I am not sure about the format of the input file : I'm trying with a txt file shaped like this :
Ensembl_Gene_ID Gene_Symbol log2FC_DeSeq p_DeSeq padj_DeSeq
ENSG00000090339 ICAM1 6,5146051234 0 0
ENSG00000108691 CCL2 6,3686974669 0 0
ENSG00000118503 TNFAIP3 4,142184042 0 0
I'm still not sure if I'm using the good table of data, because the groupGo and enrichGo functions do not work.
I did :
data <- read.table("human_retine.txt", header=TRUE, dec=",") # Gene Ontology classification genes <- data$Ensembl_Gene_ID genes <- as.character(genes) ggo <- groupGO(gene = genes, organism = "human", ont = "BP", level = 3, readable = TRUE) # Enrich GO genes<-data$Ensembl_Gene_ID[abs(data$log2FC_DeSeq)>2] ego <- enrichGO(genes , organism= "human", ont= "CC", pAdjustMethod="BH", pvalueCutoff=0.1, qvalueCutoff=0.5, readable= TRUE)
First, I had the following error when launching groupGo :
Error in validObject(.Object) : invalid class “groupGOResult” object: invalid object for slot "gene" in class "groupGOResult": got class "factor", should be or extend class "character"
So I add the as.character line, which gave me :
Error in .testForValidKeys(x, keys, keytype) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.
Then, when I launch enrichGo, the result is [NA], wheter or not the as.character function has been called.
So, it is really messy for me ... what am I doing wrong ? I am reading the docs but I don't understand all of it.