Question: Galaxy cummeRbund fails to identify sample name for X and Y axis for scatter and volcano plot
2
gravatar for deepak.bharti03
12 weeks ago by
deepak.bharti0320 wrote:

Hello, I have cuff diff sqlite db for 2 samples and I wish to visualise the result using galaxy-cummeRbund. I have no issue to get plots like density, dendrogram, PCA , and box plot but when I want to use scatter plot and volcano plot ,it fails to identify the name for X and Y axis (no options available ). Can someone please help me to know what I am doing wrong?

NOTE : I followed tuxedo pipeline in galaxy for RNASeq analysis. There are no biological replicates only two samples, control and treated one.

ADD COMMENTlink modified 4 days ago by Jennifer Hillman Jackson23k • written 12 weeks ago by deepak.bharti0320

I have the same problem. Has this been answered?

ADD REPLYlink written 11 days ago by adh9940

Not yet. But when I used the generated sql file for analysis purpose outside of galaxy it works. unfortunately there are not much information on galaxy standard error log so I don't know what is the actual problem. honestly I did not go to look entire R script of galaxy-cummerbund so unable to say what actually wrong with data or script.

ADD REPLYlink written 11 days ago by deepak.bharti0320
0
gravatar for Jennifer Hillman Jackson
4 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

This tool is problematic right now. The issues involve graphing in general and any query that filters by gene id. Please follow this ticket for updates: https://github.com/galaxyproject/tools-devteam/issues/340

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 days ago by Jennifer Hillman Jackson23k

Thanks for the update.

ADD REPLYlink written 4 days ago by deepak.bharti0320
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