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  • mastal
    replied
    The thing to do is to try a simple sql command that should return a small number of results.

    For example:
    sql <- SELECT * FROM gpl LIMIT 10

    And when reporting errors with R, you should always give the results of sessionInfo().

    Leave a comment:


  • eslamais
    replied
    I think it actually worked.

    I want to see how many rna-seq platform are in GEO that are time series and apparntly nothing.

    Unless the coding is wrong and has to indicate something else.

    Leave a comment:


  • eslamais
    replied
    I am using R studio if that you mean.

    I changed the code a little, now there is no error but also no result.

    But I am seeing some result in tables, I want to see ll of them an dI am sure there are more than a few row including this condition.

    > sql <- paste ("SELECT DISTINCT ",
    + "gpl.ID, gds.platform_technology_type ",
    + "FROM ",
    + "gpl ",
    + "JOIN ",
    + " gds ON gds.gpl = gpl.gpl ",
    + "JOIN ",
    + "gds_subset ON gds.gds = gds_subset.gds ",
    + "WHERE ",
    + " gds_subset.type LIKE '%time%' AND ",
    + "gpl.technology LIKE '%high-throughput%'",sep="")
    > rs <- dbGetQuery(con,sql)
    > dim(rs)
    [1] 0 2
    > rs
    [1] ID platform_technology_type
    <0 rows> (or 0-length row.names)

    Leave a comment:


  • mastal
    replied
    Are you running R interactively, and if so, at what stage are you getting the error message?

    Leave a comment:


  • eslamais
    replied
    THANKS MASTAL

    I changed the code as you said

    however, I still get the error

    sql <- paste("SELECT DISTINCT ",
    "gpl.ID ",
    "gds.platform_technology_type ",
    "FROM ",
    "gpl ",
    "JOIN ","gds_subset ON gds.gds = gds_subset.gds ",
    "JOIN ","gds ON gds.gpl = gpl.gpl ",
    "WHERE ",
    "gds_subset.type LIKE 'time' ",
    "AND ",
    "gpl.technology LIKE 'high-throughput sequencing' ",sep="" )



    rs <- dbGetQuery(con,sql)
    rs

    Leave a comment:


  • mastal
    replied
    I am not sure what is causing the error message, because the code you showed doesn't go as far as submitting the sql query, but there are a couple of problems with your SQL SELECT statement.

    You have 2 WHERE clauses in the SELECT statement. What you should have is the two parts of the WHERE clause separated by AND. So remove the second 'WHERE' and replace with 'AND'.

    Your second JOIN statement looks like it is a typo and you should probably have

    JOIN ","gds ON gds.gpl = gpl.gpl ",

    instead of
    JOIN ","gpl ON gds.gpl = gpl.gpl ",

    Have a look at the examples in the documentation for GEOmetadb.

    Leave a comment:


  • eslamais
    replied
    Error in sqliteSendQuery(con, statement, bind.data) :
    error in statement: near ".": syntax error

    Leave a comment:


  • eslamais
    started a topic Do you know what is this queri problem?

    Do you know what is this queri problem?

    source("http://bioconductor.org/biocLite.R")
    biocLite("GEOmetadb")

    library(GEOmetadb)

    ###################################################################################################
    # Connect with the DB
    ###################################################################################################

    con <- dbConnect(SQLite(),'GEOmetadb.sqlite')

    sql <- paste("SELECT DISTINCT ",
    "gpl.ID ",
    "gds.platform_technology_type ",
    "FROM ",
    "gpl ",
    "JOIN ","gds_subset ON gds.gds = gds_subset.gds ",
    "JOIN ","gpl ON gds.gpl = gpl.gpl ",
    "WHERE ",
    "gds_subset.type LIKE 'time' ",
    "WHERE ",
    "gpl.technology LIKE 'high-throughput sequencing' ",sep="" )


    It gave me this error:
    Error in sqliteSendQuery(con, statement, bind.data) :
    error in statement: near ".": syntax error

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