[BioC] RMySQL, for loop problem...

[Cui, Wenwu (NIH/NLM/NCBI) [C]]

Try to printout your command before execute the query:

for (i in 1:nrow(geni_FClow)){

Sqlcmd <- paste("update GO_DC5_vs_50PC3_apoptosis set FC_low = ", 
geni_FClow$FC_low[i], " where geni like ", geni_FClow$geni[i], sep =
"");

Sqlcmd;

#dbSendQuery(con, Sqlcmd)
 }

You might need to add the \" before and after geni_FClow$geni[i].

Wenwu Cui, PhD
National Center for Biotechnology Information
National Institutes of Health

-----Original Message-----
From: Alessandro Bruselles [mailto:a.bruselles at gmail.com] 
Sent: Monday, June 18, 2007 9:20 AM
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] RMySQL, for loop problem...

This is the object I want to read from:
 > geni_FClow
      geni  FC_low
1 AF039390 -1.704
2 AF039390 -1.704
3 AF116456  1.501
4 AJ250915  1.656
5 AJ250915  1.656
6 AF326592  1.835

This is the command I'm trying to use (as Cui, Wenwu suggested)
 > Sqlcmd <- paste("update GO_DC5_vs_50PC3_apoptosis set FC_low = ", 
geni_FClow$FC_low[i], " where geni like ", geni_FClow$geni[i], sep = "")
 > for (i in 1:nrow(geni_FClow)){
+ dbSendQuery(con, Sqlcmd)
+ }

and this is the error I get:
Errore in mysqlExecStatement(conn, statement, ...) :
        RS-DBI driver: (could not run statement: Unknown column 
'AF039390' in 'where clause')

 > is.data.frame(geni_FClow)
[1] TRUE

Thanks

Alessandro


Sean Davis ha scritto:
> Alessandro Bruselles wrote:
>   
>> 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,
>
> You will probably want to post the code that you tried and what errors
> you received.  The way you are trying is the correct way of performing
> the update, but there are a few details to get right before it will
work.
>
> Sean
>
>   

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