Error with connected perturbations analysis

[Lape, Mike (lapema)]

Hello.

 

Is there a minimum number of genes required for the “Connected LINCS chemical perturbagens” analysis tool? I ask because I’ve run a few lists of genes with success but when trying to run this smaller one with just 16 genes, I keep getting the error, “The analysis end up with an error: Error in iLincsR sigEnrichment function”. I’ll put my up and down-regulated gene lists below.

 

Up:

2070

10736

2624

101927167

7058

3429

23581

4046

8542

7348

51200

 

Down:

6493

5069

101927953

63951

50486

 

Thank you for your help.

Mike Lape

[mbfazel]

Hi Mike,

I'm not sure if you have figured this out yet, but here is the answer: yes, there should be more than two genes to complete this analysis and the list you are submitting has only one gene in common with L1000 data. If you go to "Connected Signatures" tab before you go to "Connected Perturbations" tab, you'll see there is only one gene in common with LINCS signatures and that's why.

Hope this helps,

Mehdi