Question: SQLite file from Galaxy gives "0 obs."
0
gravatar for eculfa
4 weeks ago by
eculfa0
eculfa0 wrote:

Hello!

After I have performed Cuffdiff in Galaxy on my two RNA-Seq data of different treatment conditions, I loaded my SQLite data into RStudio to see the differentially expressed genes. However, after I command; "gene_diff_data <- diffData(genes(cuff_data))" I don't see any data available in R. The only available info in R is "0 obs. in 11 variables". What could be the reason for this? Where have I done wrong? My galaxy run progressed pretty smoothly.

Thank you! Efraim

rna-seq sqlite R • 79 views
ADD COMMENTlink modified 12 days ago • written 4 weeks ago by eculfa0
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

You probably need to initialize the cuff_data object first:

cuff_data<-readCufflinks()

or skip the underscore and keep the name simple to use in downstream functions:

cuff<-readCufflinks()

Reference: http://compbio.mit.edu/cummeRbund/manual_2_0.html

Hope that helps! Jen, Galaxy team

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Jennifer Hillman Jackson23k
0
gravatar for eculfa
12 days ago by
eculfa0
eculfa0 wrote:

hi! I have followed the instructions that you gave but it still wouldn't work. In the meantime, I have googled to see if others had experienced similar problems to find there doesn't seem to be a step by step troubleshooting of the problem. Later on, I tried to get my figures in galaxy but it was to no avail. I got this error after I tried to run cummeRbund on galaxy; "Attempting to run a tool with empty command definition." I later on read that it might be a bug ; https://github.com/galaxyproject/tools-devteam/issues/340 Since I had failed on both platforms, could it be due to one of the galaxy tools I used during my processing of data?

Thank you so much for the quick feedbacks! I truly appreciate Galaxy Team's effort! Efraim

ADD COMMENTlink written 12 days ago by eculfa0

Yes, graphing this data is not possible until the fix. The ticket you are following will be updated and closed once done. Thanks, Jen, Galaxy team

ADD REPLYlink written 12 days ago by Jennifer Hillman Jackson23k
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