Confusion about inputs for CARNIVAL about carnival HOT 5 CLOSED

Hi @anu-bioinfo,

Can you let us know what is your samples - is it bulk RNA-seq data, are those samples replicates? What is the question that you are trying to answer?

Olga

from carnival.

Hey @ivanovaos

Thanks for your quick response. These are bulk RNA-seq data. These samples are biological replicates. 4 for treatment and 4 for control.
Hence, for both DOROTHEA and PROGENY I get a 8 * n matrix (8 being the total number of samples and n being the number of TFs/Pathways)

Basically, I am comparing the treatment samples with control samples. I wish to find TFs/PPIs/networks which drive the phenotypic difference between the control and the treatment group.

Thanks for any help.

Regards,

Anupam

from carnival.

Hi @anu-bioinfo,

Are they paired one to one? How many networks you want to get out of CARNIVAL - 4, 8, or 1?

You can treat this type of analysis with different approaches. If it is 4 networks you want to get, basically the output of CARNIVAL is a network explaining the difference for paired conditions. If it is 8 networks, you get the output explaining each sample, and then you apply network approaches to compare conditions. If it is 1 network, it would be explaining the difference between the averaged signals among 4 treatments/4 controls.

If it is the first and last case, you need to run DoRoThEA/VIPER on contrasts (not on expression matrices). Then you need to run CARNIVAL as many times as you have inputs (4 or 8, 1).

Is this helpful?

Also, there is a new tutorial for all tools here

from carnival.

@anu-bioinfo Did it help? Do you need more guidance or we can close the issue?

from carnival.

Hi @ivanovaos

Thanks a lot for the tutorial and the message it was really helpful.

from carnival.