goseq: In pcls(G) : initial point very close to some inequality constraints
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@heikkisarin-13379
Last seen 8 months ago

Hi,

I'm running pathway analysis with goseq but had the error : In pcls(G) : initial point very close to some inequality constraints : when plotting the nullp. I'm not sure if this is an issue or not. The curve doesn't start on the y-axin from zero but 0.004 but after that the curve is pretty similar to the ones in examples. However, the dots are plotted quite randomly across the field.

Is this a concern and if is how might I solve this?

Despite this the results seem to match to our differential expression analysis results.

Really appreciate the help!

 

goseq warning message pwf mgcv • 1.8k views
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@nadia-davidson-5739
Last seen 2.4 years ago
Australia

Hi,

You should not need to worry about this warning as long as the plotted nullp function looks fine and it sounds like it is okay in your case. If the dots look random, it might be that there's very little gene length bias in your data, in which case the fitted curve should be mostly flat.

 

Cheers,

Nadia.

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