[BioC] RMySQL, for loop problem...

Peter Sørensen (HAG) Peter.Sorensen2 at agrsci.dk
Mon Jun 18 12:57:06 CEST 2007

assemble the sql command first as suggested by others and then use the dbSendQuery function.
dbSendQuery(con, Sqlcmd)
this used to work for me



Fra: bioconductor-bounces at stat.math.ethz.ch på vegne af Alessandro Bruselles
Sendt: ma 18-06-2007 12:04
Til: Bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] RMySQL, for loop problem...

Thanks to all who tried to help me,
but none of the suggested solutions worked for me,
I still didn't manage to do the loop...
How else can I do to iteratively update my db?

Alessandro Bruselles
University of Rome "Tor Vergata"

Herve Pages ha scritto:
> Hi Alessandro,
> Alessandro Bruselles wrote:
>> I'm trying to do a little loop using the RMySQL package to update some
>> fields in my db
>> but I can't find a way;
>> the loop should be this:
>> /for (i in 1:nrow(geni_FClow)){
>>    dbGetQuery(con, "update GO_DC5_vs_50PC3_apoptosis set FC_low =
>> geni_FClow$FC_low[i] where geni like geni_FClow$geni[i]")
>> }/
> R is not PHP ;-)
>   > x <- "'letters[1]' is the first letter of the latin alphabet"
>   > x
>   [1] "'letters[1]' is the first letter of the latin alphabet"
> No variable substitution in string 'x'. That's why you don't get
> this:
>   [1] "'a' is the first letter of the latin alphabet"
> Cheers,
> H.
>> but I get the following error:
>> /Errore in mysqlExecStatement(conn, statement, ...) :
>>         RS-DBI driver: (could not run statement: You have an error in
>> your SQL syntax; check the manual that corresponds to your MySQL server
>> version for the right syntax to use near '[i] where geni like
>> geni_FClow$geni[i]' at line 1)/
>> while the simple statement:
>> /dbGetQuery(con, "update GO_DC5_vs_50PC3_apoptosis set FC_low =
>> geni_FClow$FC_low[2] where geni like geni_FClow$geni[2]")/
>> (using a number instead of the [i])
>> works!
>> Any help would be appreciated
>> (I know maybe the answer is so simple I cannot see it...)

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