[lgoff]

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

[AddDNAse]

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:

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:

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).

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!

[david.eby]

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):

      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:

      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!

[NRB]

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