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giannimonaco / ABIS

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RLM Warning message when running ABIS locally on a large dataset #19

Open sam-israel opened 3 years ago

sam-israel commented 3 years ago

I have cloned the repo ( git clone https://github.com/giannimonaco/ABIS) and ran the Shiny app locally (leaving all files as they are without change) - on 400 human samples.

I get a message

Warning in rlm.default(as.matrix(sigRNAseq[genes, ]), x, maxit = 100) :
  'rlm' failed to converge in 100 steps

Is it important? Does it invalidate the deconvolution results? How can this be fixed?

giannimonaco commented 3 years ago

Hi, the results should still be good even if you get the warning. You could increase the value given to the maxit argument to avoid the warning.

On Mon, 7 Jun 2021 at 10:26, sam-israel @.***> wrote:

I have cloned the repo ( git clone https://github.com/giannimonaco/ABIS) and ran the Shiny app locally (leaving all files as they are without change) - on 400 samples.

I get a message

Warning in rlm.default(as.matrix(sigRNAseq[genes, ]), x, maxit = 100) : 'rlm' failed to converge in 100 steps

Is it important? Does it invalidate the deconvolution results? How can this be fixed?

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