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Old 05-14-2014, 01:57 PM   #32
AddDNAse
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Location: Wisconsin

Join Date: May 2014
Posts: 3
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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).

Quote:
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 at 02:02 PM.
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