Re: [Seqbuster-questions] miRNA analysis problem

[Lorena P. <lor...@gm...>]

Hi,

Thank you very much to ask me. I will be out of office during the morning,
but this afternoon I will check the code to see if there is any bug, since
updated last friday maybe I introduce a bug.

One question, did you change any parameter?

I will come back today

cheers

Lo


On Wed, Feb 22, 2012 at 12:39 AM, Bruce, Can John <can...@ya...>wrote:

>  Hello,****
>
> ** **
>
> I am going through the test data set to familiarize myself with seqbuster.
> In the miRNA analysis step I got the following error message in the
> IsoseqDistribution.Rout file:****
>
> ** **
>
> ==============================****
>
> [1] "select
> `id`,`chr`,`freq`,`trimmed5`,`trimmed3`,`addition3`,`mut`,`trimmed3ref`,`trimmed5ref`
> from `testpro`.`testr`  `freq` >= 0.****
>
> 01  AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND  `mut` NOT REGEXP
> '^0[ACTG]+' AND  `mut` NOT REGEXP '^-[0-9]+[ACTG]+' AND `mut`****
>
> NOT REGEXP '^[0-9]+[ACTG]+[0-9]+';"****
>
> Error in mysqlExecStatement(conn, statement, ...) : ****
>
> (could not run statement: You have an error in your SQL syntax; check the
> manual that corresponds to your MySQL serve****
>
> r version for the right syntax to use near '>= 0.01  AND `DB` LIKE 'miRNA'
> AND `chr` NOT LIKE 'amb' AND  `mut` NOT REGEXP '^' at line ****
>
> 1)****
>
> Calls: dbSendQuery ... .valueClassTest -> is -> is -> mysqlExecStatement
> -> .Call****
>
> Execution halted****
>
> ========================****
>
> ** **
>
> Am I doing something wrong? is there a "WHERE" missing in the SQL query
> above?****
>
> ** **
>
> ** **
>
> Can Bruce****
>
> Bioinformatics Resource****
>
> Keck Lab****
>
> Yale University****
>
> ** **
>
>
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