Question: MeSH enrichment analysis with "meshes"
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gravatar for ayatrience
10 months ago by
ayatrience0
ayatrience0 wrote:

I wanted to do MeSH enrichment analysis with "meshes" package designed by Guangchuang YU. However, I entered like below following description of "meshes" in R,

result <- enrichMeSH(gene = degsentrez, universe = allentrez, MeSHDb = "MeSH.db",database = "Gendoo",category = "A", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff =0.05)

error messages come; "no such column: GENEID".

What is wrong with my code? Degsentrez & allentrez are column vector of entrez gene ID as description requires I think.

meshes • 247 views
ADD COMMENTlink written 10 months ago by ayatrience0

what's the output of traceback() immediately run after the error appear?

ADD REPLYlink written 10 months ago by Guangchuang Yu1.1k

This is the output.

16: stop(list(message = "no such column: GENEID", call = resultcreate(conn@ptr, statement), cppstack = list(file = "", line = -1L, stack = "C++ stack not available on this system"))) 15: resultcreate(conn@ptr, statement) 14: initialize(value, ...) 13: initialize(value, ...) 12: new("SQLiteResult", sql = statement, ptr = resultcreate(conn@ptr, statement), conn = conn, bigint = conn@bigint) 11: .local(conn, statement, ...) 10: dbSendQuery(conn, statement, ...) 9: dbSendQuery(conn, statement, ...) 8: .local(conn, statement, ...) 7: dbGetQuery(x$conn, query) 6: dbGetQuery(x$conn, query) 5: .local(x, keys, columns, keytype, ...) 4: select(db, keys = database, columns = c("GENEID", "MESHID", "MESHCATEGORY"), keytype = "SOURCEDB") 3: select(db, keys = database, columns = c("GENEID", "MESHID", "MESHCATEGORY"), keytype = "SOURCEDB") 2: getMeSH_data(MeSHDb, database, category) 1: enrichMeSH(gene = degs.entrez[, 2], universe = all.entrez[, 2], MeSHDb = "MeSH.db", database = "Gendoo", category = "A", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05)

but, perhaps I can do that correctly, when I change to the MeSH.db for mice "MeSH.Mmu.eg.db" and database = "gendoo" it seems to work correctly and I can get something like result by head().

Thank you very much for your answer and sorry for troubling you if this comes from my lack of knowledge of R language.

ADD REPLYlink written 10 months ago by ayatrience0
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