Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • #2
    Error in sqliteSendQuery(con, statement, bind.data) :
    error in statement: near ".": syntax error

    Comment


    • #3
      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.

      Comment


      • #4
        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

        Comment


        • #5
          Are you running R interactively, and if so, at what stage are you getting the error message?

          Comment


          • #6
            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)

            Comment


            • #7
              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.

              Comment


              • #8
                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().

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Exploring the Dynamics of the Tumor Microenvironment
                  by seqadmin




                  The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                  07-08-2024, 03:19 PM
                • seqadmin
                  Exploring Human Diversity Through Large-Scale Omics
                  by seqadmin


                  In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                  06-25-2024, 06:43 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 07-16-2024, 05:49 AM
                0 responses
                20 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-15-2024, 06:53 AM
                0 responses
                29 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-10-2024, 07:30 AM
                0 responses
                40 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-03-2024, 09:45 AM
                0 responses
                205 views
                0 likes
                Last Post seqadmin  
                Working...
                X