Question

GOseq warning message.

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Pauly Lin ▴ 160

@pauly-lin-7537

Last seen 9.2 years ago

University of New South Wales, Australia

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?

Cheers

Paul

goseq • 2.6k views

ADD COMMENT • link updated 9.5 years ago by Nadia Davidson ▴ 320 • written 9.5 years ago by Pauly Lin ▴ 160

score 1 · Accepted Answer · 2015-06-22

1

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Nadia Davidson ▴ 320

@nadia-davidson-5739

Last seen 5.7 years ago

Australia

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.

Cheers,

Nadia.

ADD COMMENT • link 9.5 years ago Nadia Davidson ▴ 320

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Thanks, Nadia.

Paul

ADD REPLY • link 9.5 years ago Pauly Lin ▴ 160

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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 REPLY • link 7.4 years ago heikki.sarin ▴ 10