Problems with EBSeq - density histograms and QQ plots do not appear correct

[dla...@gmail.com]

Hi all,

I've run EBSeq on human isoform data, here are the basic details:

- about 180K isoforms (human transcriptome)

- 5 conditions, each with a minimum of 7, but up to 14 biological replicates.

- 10 uncertainty groups (the toy example in the EBseq vignette using 3 groups is insufficient for human, so I upped this considerably).

- 10 iterations, all parameters (beta, alpha, P, reach convergence).

- patterns representing ubiquitous expression, and a single pattern for each tissue representing tissue specific expression (6 patterns in total).

When I run the QC on the method as per the vignette, fitted lines do not correspond with the density histograms as I would expect, and neither do the estimated vs simulated Q values fit correctly (see attached documents).

Does anyone know what is going on here or can advise?

Kind Regards,
David

[Ning Leng]

Hi David,

Is it possible to send me the data or part of your data to look into more details of this issue?

Thanks!

Ning

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Ning Leng
University of Wisconsin Madison
Department of Statistics
4720 Medical Sciences Center
1300 University Avenue
Madison, Wisconsin 53706

[Julie]

Hi Guys,

Just wandering whether you find out the reasons? I just got a similar strange plots, looks like the alpha and beta values exchanged?

Julie