FourCseq and local fit
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tlgolan • 0
@tlgolan-10804
Last seen 5.0 years ago

Hi,

I am trying to analyze my 4Cseq data using the FourCseq package. 

I have some difficulties while running the getZscores function; I keep getting this Error: 

gene-wise dispersion estimates

mean-dispersion relationship

-- note: fitType='parametric', but the dispersion trend was not well captured by the

   function: y = a/x + b, and a local regression fit was automatically substituted.

   specify fitType='local' or 'mean' to avoid this message next time.

final dispersion estimates

Error in getZScores(fc, removeZeros = TRUE, minCount = 0, fitFun = distFitMonotone) : 

Failed to estimate the parameters of the Variance stabilizing transformation.

 

The weird thing is that I succeeded to transform my data by using varianceStabilizingTransformation function (DESEQ2).

I read that currently the FourCseq analysis does not work with a local fit (Felix's remark on the bioconductor forum, 7 months ago). Is it still relevant? If the answer is yes, do you have any recommendations on how I can proceed with the analysis?

fourcseq • 408 views
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