Re: [Seqbuster-questions] miRNA analysis problem

[Bruce, C. J. <can...@ya...>]

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...<mailto: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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