Error while running clusterProfiler

Question

[bioinfo8]

Hi,

I am trying to run clusterProfile after installing all dependencies and when I run:

ggo <- clusterProfiler::groupGO(gene = gene, OrgDb = org.db, ont = "BP", level = 3, readable = TRUE)

I get the following error:

Error in rsqlite_send_query(conn@ptr, statement) : 
  external pointer is not valid

Please guide Guangchuang Yu.

Thanks.

Answer 1

[Guangchuang Yu]

You did not provide the information of your org.db and the error msg indicates that it can't access sqlite file of your org.db.

[bioinfo8]

Thanks for the hint. I managed to solve. But now, getting another error from the same command Guangchuang Yu :

Error in validObject(.Object) : 
  invalid class “groupGOResult” object: invalid object for slot "gene" in class "groupGOResult": got class "data.frame", should be or extend class "character"

I used the following code (df_0.05 is the dataframe from DESeq2 output containing entries with padj < 0.05):

geneList <- as.vector(df_0.05$log2FoldChange)
names(geneList) <- df_0.05$entrezgene
ggo <- clusterProfiler::groupGO(gene = gene, OrgDb = org.my_species.eg.db, ont = "BP", level = 3, readable = TRUE)

[bioinfo8]

I figured out and it worked:

gene_char <-  as.character(gene$entrezgene)
ggo <- clusterProfiler::groupGO(gene = gene_char, OrgDb = org.my_species.eg.db, ont = "BP", level = 3, readable = TRUE)