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  • #31
    Originally posted by AddDNAse View Post
    Hi everyone,

    I hope someone is still checking this thread. I am having a very similar problem. I have tried all of the troubleshoots posted here. I keep getting the following:
    tracking_id gene_short_name
    1 XLOC_000010 <NA>
    2 XLOC_000011 <NA>
    3 XLOC_000013 <NA>
    4 XLOC_000014 <NA>
    5 XLOC_000018 <NA>
    6 XLOC_000022 <NA>
    Hi AddDNAse, Can you provide a bit more context here. How are you generating this list of tracking_id and gene_short_names. Can you find a gene by gene_short_name using findGene()? Can you post a bit more of the code to provide a better description of what's going on.

    Thanks,
    Loyal

    Comment


    • #32
      Hi Loyal,

      First of all, I'm using the S. cerevisiae annotation and genome from Ensembl (found on the Cufflinks website). I have modified the annotation to include a few smallRNAs.

      This list I posted was done using the following code:
      Code:
      gene_diff_data<-diffData(genes(cuff_data))
      sig_gene_data<-subset(gene_diff_data, (significant == 'yes'))
      diffGenes<-getGenes(cuff_data, sig_gene_data$gene_id)
      head(featureNames(diffGenes),n=3)
      I also tried doing the following:
      Code:
      gene.features<-annotation(genes(cuff))
      head(gene.features)
      Where I get the same result (almost all are 'NA' for gene_short_name with a few exceptions).

      Originally posted by lgoff View Post
      Hi AddDNAse, Can you provide a bit more context here. How are you generating this list of tracking_id and gene_short_names. Can you find a gene by gene_short_name using findGene()? Can you post a bit more of the code to provide a better description of what's going on.

      Thanks,
      Loyal
      Hope this is enough info? Thanks!
      Last edited by AddDNAse; 05-14-2014, 02:02 PM.

      Comment


      • #33
        Hi everyone,

        I'm just posting this for the benefit of anyone looking for help on the topic in the future. I worked out a variation of the code posted earlier by Thomas but modified to handle merging in the face of duplicate lines in the table. Here's a simplified version of what we're using in GenePattern for the CummeRbund.QcReport module (currently in Beta):
        Code:
              feature.level <- "genes"
                 # ... or "isoforms", "TSS", "CDS"
              idColumnName <- "gene_id"
                 # ... or "isoform_id", "TSS_group_id", "CDS_id" to match above
              report.name <- paste0('QC.sig_diffExp_', feature.level,'.txt')
                 # ... or whatever you want
              
              cuff <- readCufflinks()
              sigIDs <- getSig(cuff,level=feature.level,alpha=0.05)
              if (NROW(sigIDs) > 0) {
                 sigFeatures <- getFeatures(cuff,sigIDs,level=feature.level)
                 sigData <- diffData(sigFeatures)
                 sigData <- subset(sigData, (significant == 'yes'))
                 names <- featureNames(sigFeatures)
                 sigOutput <- merge(names, sigData, by.x="tracking_id", 
                                    by.y=idColumnName)
                 
                 # Patch the merged table to have the original name for the ID column.  
                 # This is always the first column for the examples we've seen.
                 colnames(sigOutput)[1] <- idColumnName
                 write.table(sigData, report.name, sep='\t', row.names = F, 
                             col.names = T, quote = F)
              }
        The point here is to write a report file containing the table, but one could obviously use the sigOutput object directly instead.

        Here is similar code to do likewise for the distValue reports:
        Code:
              dist.selector.function <- promoters
                 # ... or splicing or relCDS
                 # Note that this is a function name, not a String!
              feature.level <- "genes"
                 # use "isoforms" for splicing, "genes" for promoter and relCDS
              report.name <- "QC.sig_promoter_data.txt"
                 # ... or whatever you want
        
              distData <- distValues(dist.selector.function(cuff))
              sigData <- subset(distData, (significant == 'yes'))
              if (nrow(sigData) > 0) {
                 sigIDs <- sigData[[1]]
                 sigFeatures <- getFeatures(cuff,sigIDs,level=feature.level)
                 names <- featureNames(sigFeatures)
                 sigOutput <- merge(names, sigData, by.x="tracking_id", 
                                    by.y=idColumnName)
                 colnames(sigOutput)[1] <- idColumnName
                 write.table(sigData, report.name, sep='\t', row.names = F, 
                             col.names = T, quote = F)
              }
        Just for reference, the above is for R 2.15.3, Bioconductor 2.11 and cummeRbund 2.0.0. Hope it helps someone!

        Comment


        • #34
          Hi can someone help me. I am student still learning on R. Doing a DEG analysis. i want to visualize my DEG data got from cuffdiff 2.0... When want to create Gene Set Obeject, an error occurs


          enes<-getGenes(cuffCan,myGeneIds)
          Getting gene information:
          FPKM
          Error: near ")": syntax error
          In addition: Warning message:
          Closing open result set, pending rows



          Im not sure where is the syntax error. Could someone guide me through it

          Comment

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