Question: Deseq2 experimental layout
0
gravatar for VY
19 months ago by
VY120
United States
VY120 wrote:

Hello,

This isn't entirely a bioinformatic related question but if anyone has any input it would be greatly appreciated.

I have 3 libraries, each of the same FACS sorted cells, under the same conditions, with the difference that each library was done on cells isolated at different time points, and we don't have replicates. I've generated count files for each of the libraries but I'm having issues as to how to lay them out into deseq2 on galaxy.

My initial approach was to set them all out under the same Factor name, in different factor levels:

E.g Factor name: Neurons Factor level 1: 3h 2: 6h 3: 12h

But that layout seemed to not be working out that well all the outputs seemed odd as it was skipping factor level 3 in the comparison.

I tried setting each time point under a different factor name but the issue there is that Deseq2 required at least 2 factor levels for each factor name.

Any suggestions how to go about analysing this?

Best wishes

rna-seq deseq2 • 501 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by VY120
1
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

To include more than two factor levels, this option should be set to "Yes". enter image description here

Is this problematic for you? If so, consider sending in a bug report, there could be a tool problem. The shared analysis will also be reviewed for usage issues. Please include a link to this post in the comments if you do send one in. https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Best, Jen, Galaxy team

ADD COMMENTlink modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson23k
0
gravatar for VY
19 months ago by
VY120
United States
VY120 wrote:

Hey

Thanks for the feedback. I tried it again now and it all seems to have worked. Probably a momentary glitch. Thanks Jennifer!

ADD COMMENTlink written 19 months ago by VY120
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