GabrielHoffman/variancePartition

Issues

• Encountered an error when running the example, and my matrix package was version 1.6-1.1.

  #100 opened 4 months ago by fengqlin
  1

• Large difference in results between v1.28.9 and v1.35.3

  #99 opened 5 months ago by alexvpickering
  6

• Enable fitting of non-full rank formula

  #95 opened 5 months ago by jmichuda
  3

• voomWithDreamWeights() does not work with raw counts

  #97 opened 5 months ago by yonbar
  4

• Error in if (inherits(possibleError, "error") && grep("the fixed-effects model matrix is column rank deficient", : missing value where TRUE/FALSE needed

  #96 opened 5 months ago by sdwang008
  2

• Warning message: In .standard_transform(ret): No testable fixed effects were included in the model.

  #98 opened 5 months ago by JEJKarppinen
  3

• p-values

  #90 opened 8 months ago by palbioinfor
  4

• Issue with failing responses and Kenward-Roger method

  #92 opened 8 months ago by hayleywelsh
  23

• Parameters to increase iterations for model fitting of genes

  #94 opened 8 months ago by shoffm
  3

• voomWithDreamAndQualityWeights?

  #87 opened 8 months ago by knokknok
  1

• Adjusting R2

  #86 opened 8 months ago by MEladawi
  2

• Can this be used on scRNA-seq dataset?

  #93 opened 10 months ago by Jiayi-Zheng
  4

• RStudio/BiocParallel warning cause execution to crash

  #91 opened a year ago by yonbar
  4

• Questions about P.values

  #89 opened a year ago by Jayanth-Sreekanth
  4

• Error in checkModelStatus(fitInit, showWarnings = showWarnings, colinearityCutoff = colinearityCutoff) : boundary (singular) fit: see help('isSingular')

  #77 opened a year ago by Jason-bot-stack
  0

• dream(): Evaluate function error --> "Error evaluating fxn:"

  #66 opened 2 years ago by aidarripoll
  14

• BiocParallel

  #73 opened 2 years ago by nickhsmith
  1

• Error in if (inherits(possibleError, "error") && grep("the fixed-effects model matrix is column rank deficient", : missing value where TRUE/FALSE needed

  #72 opened 2 years ago by stanleyjs
  4

• just the toy dataset example not working.

  #71 opened 2 years ago by zntaylgit
  2

• collinearity issue

  #70 opened 2 years ago by jonahcullen
  2

• p-values of the correlation from "canCorPairs"

  #69 opened 2 years ago by se2cheeese
  2

• There are NA values -- Missing data is not allowed

  #68 opened 2 years ago by DMPKendo
  1

• Assessing significance of genes

  #67 opened 2 years ago by jcgrenier
  4

• equivalent parameterization of the fix effects lead to different estimates

  #65 opened 2 years ago by coralzhang
  1

• Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

  #64 opened 2 years ago by evaesquinas
  8

• How to use BiocParallel and variancePartition?

  #63 opened 2 years ago by evaesquinas
  4

• Can variancePartition handle TPM normalized counts as the input?

  #62 opened 2 years ago by evaesquinas
  5

• Remove batch effect before fitting the model

  #59 opened 2 years ago by evaesquinas
  10

• Can variancePartition be used for analyzing single-cell data?

  #61 opened 2 years ago by DongzeHE
  2

• Error encountered when running the example dataset

  #60 opened 2 years ago by DongzeHE
  4

• Why are my adjusted p-values all the same in my output from my dream analysis?

  #57 opened 2 years ago by dahrendorff
  2

• confint option for topTable function not working

  #58 opened 2 years ago by jcgrenier
  6

• error when running fitExtractVarPartModel()

  #56 opened 2 years ago by luthientinuviel
  4

• Analysis repeated measurement data with dream

  #35 opened 2 years ago by YouthYong
  2

• Dream function: Please throw informative error message

  #36 opened 2 years ago by arnaudmgh
  2

• Using fitExtractVarPartModel with lmer/glm/negbin

  #42 opened 2 years ago by LunavdL
  4

• underlying assumptions input data

  #43 opened 2 years ago by guidohooiveld
  1

• to evaluate the significance on random effect、

  #45 opened 2 years ago by chengarthur
  1

• Hi, Is there a way to use the Dream package to test for Differential Transcript Usage

  #49 opened 2 years ago by niradsp
  5

• inclusion of eBayes shrinkage step for dream mixed models

  #54 opened 2 years ago by MattPM
  3

• Error with plotStratify()

  #55 opened 2 years ago by mikemwanga
  4

• boundary (singular) fit: see help('isSingular')

  #53 opened 2 years ago by se2cheeese
  4

• Use in proteomics

  #52 opened 2 years ago by AUldry
  2

• possible test failure with development version of lme4

  #51 opened 3 years ago by bbolker
  7

• Likelihood ratio test?

  #50 opened 3 years ago by lucia-ramirez
  6

• Confidence intervals of log2(Fold_Change)

  #48 opened 3 years ago by jgockley62
  3

• R can't find makeContrastsDream

  #47 opened 3 years ago by bl24
  2

• how to manualy define order in plotStratify() ?

  #46 opened 3 years ago by guidohooiveld
  4

• Can microarray type normalized and transformed data be used as input to dream like with limma?

  #44 opened 3 years ago by hermidalc
  1

• Installation error

  #41 opened 3 years ago by guray003
  1