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wejlab / BatchQC

Batch Effects Quality Control Software
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Volcano Plot not functioning w/Example Data #59

Closed jessmcc22 closed 6 months ago

jessmcc22 commented 1 year ago 
converting counts to integer mode
  the design formula contains one or more numeric variables with integer values,
  specifying a model with increasing fold change for higher values.
  did you mean for this to be a factor? if so, first convert
  this variable to a factor using the factor() function
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
Warning: Error in estimateDispersionsFit: all gene-wise dispersion estimates are within 2 orders of magnitude
  from the minimum value, and so the standard curve fitting techniques will not work.
  One can instead use the gene-wise estimates as final estimates:
  dds <- estimateDispersionsGeneEst(dds)
  dispersions(dds) <- mcols(dds)$dispGeneEst
  ...then continue with testing using nbinomWaldTest or nbinomLRT
  2: shiny::runApp
  1: BatchQC