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
-- 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?