Question: Understanding Sleuth output for multiple samples
1
gravatar for Bharat Iyengar
2.1 years ago by
Bombay, India
Bharat Iyengar260 wrote:

I have RNAseq data from 10 different condition with two biological replicates each. I have run Kallisto on all the samples with 100 bootstraps.

I passed all the samples to Sleuth for analysis with a reference table as mentioned in the "getting started" page.

sample   condition
A1         A
A2         A
B1         B
B2         B
C1         C
C2         C

...and so on.

I fitted the model as described in the "getting started" page and exported the results obtained by

results_table <- sleuth_results(so, 'reduced:full', test_type = 'lrt')

I export this table as a CSV file with columns which include p-value and q-value (and other metrics). What I do not understand is what do these p-values signify. What happens when multiple conditions are passed; does Sleuth do a pairwise comparison? If that is so then there should be a p-value/q-value (and other values) for each pair. I am not getting that.

When I input multiple conditions then do p-values denote differential expression in all the conditions or at least one condition?

If possible also let me know (some page/resource on) what other models can be fit on the data (from the "getting started" example, it appears that different models are possible but the manual and the preprint do not mention anything other than the intercept-only model).

rna-seq kallisto sleuth • 1.9k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Bharat Iyengar260

This can be of any help: https://groups.google.com/forum/#!forum/kallisto-sleuth-users

ADD REPLYlink written 22 months ago by bioinfo8120

I posted a question there but it was not answered!

ADD REPLYlink written 22 months ago by Bharat Iyengar260
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