Re: [Seqbuster-questions] miRNA analysis problem

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

Hi,


could you run without put anything in the frequency greater or less. This
number should be integers, 0 if you want to get everything, and maybe 10 if
you want to remove sequences with lower than 10 counts.

frequency less than, greater than. less than 0.5 and greater than 0.01 it
would take nothing. 1 is the minimum.

cheers


On Wed, Feb 22, 2012 at 2:48 PM, Bruce, Can John <can...@ya...> wrote:

>  Hi Lo,****
>
> ** **
>
> The parameters were: group1=testr, Frequency greater=0.5, Frequency
> less=0.01, Select miRNA-like DB=miRNA, Contribution Cut Off=10, applied
> probabilistic model=zscore, and all checkboxes checked.****
>
> ** **
>
> By the way, does “frequency less” mean “frequency less than” or “minimum
> frequency” ?****
>
> ** **
>
> Can Bruce****
>
> Bioinformatics Resource****
>
> Keck Lab****
>
> ** **
>
> *From:* Lorena Pantano [mailto:lor...@gm...]
> *Sent:* Wednesday, February 22, 2012 3:20 AM
> *To:* Bruce, Can John
> *Cc:* seq...@li...
> *Subject:* Re: [Seqbuster-questions] miRNA analysis problem****
>
> ** **
>
> 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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> ** **
>