Question: GOseq warning message.
gravatar for Pauly Lin
3.0 years ago by
Pauly Lin80
University of New South Wales, Australia
Pauly Lin80 wrote:

Hi all,

I'm using GOseq to analyse RNASeq data. When I run the nullp function to compute PWF, I got this warning message:

"Warning message: In pcls(G) : initial point very close to some inequality constraints"

What does this warning message mean, and should I be concerned?




ADD COMMENTlink modified 3.0 years ago by Nadia Davidson270 • written 3.0 years ago by Pauly Lin80
gravatar for Nadia Davidson
3.0 years ago by
Nadia Davidson270 wrote:

Hi Paul,

This is just a warning about the initial fit parameters passed to pcls by goseq (which does the fit for pwf). Usually it is not a concern. If the fit looks reasonable in the plot produced by nullp, you can ignore this warning message.



ADD COMMENTlink written 3.0 years ago by Nadia Davidson270

Thanks, Nadia.


ADD REPLYlink written 3.0 years ago by Pauly Lin80

Had the same issue when plotting the graph. Otherwise the plot seems reasonable but the it starts from y-axis 0.004 and not from zero. Is this an issue and does it mean?

ADD REPLYlink written 10 months ago by heikki.sarin0
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