Errors in the codes from pdf OUTRIDER - OUTlier in RNA-Seq fInDER

[Paranchai]

Dear Sir/Madam

I was trying to run OUTRIDER with R following the instructions in the pdf file OUTRIDER - OUTlier in RNA-Seq fInDER, and got errors at the following steps:

map <- select(org.Hs.eg.db, keys=keys(txdb, keytype = "GENEID"), keytype="ENTREZID", columns=c("SYMBOL"))
Error in UseMethod("select") : no applicable method for 'select' applied to an object of class "c('OrgDb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass', 'environment', 'refObject', 'AssayData')"

library(RMariaDB)
library(AnnotationDbi)

con <- dbConnect(MariaDB(), host='genome-mysql.cse.ucsc.edu', dbname="hg19", user='genome')
Error: Failed to connect: Can't connect to server on 'genome-mysql.cse.ucsc.edu' (138)

then I change host to db.host and put dot to dbname, which worked but the following command did not work:

con <- dbConnect(MariaDB(), db.host='genome-mysql.cse.ucsc.edu', db.name="hg19", user='genome')
map <- dbGetQuery(con, 'select kgId AS TXNAME, geneSymbol from kgXref')
Error: No database selected [1046]

Do you know why?

I am looking forward to hearing from you soon.
Best regards
Paranchai Boonsawat

[c-mertes]

Dear @Paranchai,

as I can not reproduce your error it is hard to help you here. Could you please send me your sessionInfo() output?

Some thoughts into the blue:

• Why did you change host=xxx to db.host? This argument did not change in RMariaDB.
• Sometimes the internet connection to the UCSC database is unstable

# Can you ping it? 
ping genome-mysql.cse.ucsc.edu

# Can you connect through the command line 
# if correct it should print the host name of the database
mysql --database=hg19 --host=genome-mysql.cse.ucsc.edu --user=genome -e 'show variables like "%name%";'