rlog Posts

votes

answer

views

answer

Different PCA plots using rlog and vsd on the same data set

deseq2 pca rlog variancestabilizingtransformation plotpca written 1 day ago by lirongrossmann • 0 • updated 1 day ago by Michael Love ♦ 13k

votes

answer

228

views

answer

lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions

deseq2 rlog lfcshrink written 18 days ago by pecot • 0

vote

answer

310

views

answer

DESeq2: Difference in rlog and vst values if run transform before or after running DESeq

deseq deseq2 rlog variancestabilizingtransformation written 7 months ago by Zach Roe • 10 • updated 7 months ago by Michael Love ♦ 13k

votes

answer

343

views

answer

regularized log transformation- loss of zero values for sparsely expressed genes

deseq2 rlog variancestabilizingtransformation rlog transformation vst written 13 months ago by longwoodSequencer • 0 • updated 13 months ago by Michael Love ♦ 13k

votes

answers

585

views

answers

What does DESeq2 rlog() return exactly?

deseq2 rlog rlog transformation written 18 months ago by lanhuong • 0

votes

answers

540

views

answers

Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)

clustering cummerbund deseq2 fpkm rlog written 20 months ago by Jon Bråte • 130

vote

answer

772

views

answer

Validity of using rlog transformed counts (rld) to obtain a list of expressed genes

deseq2 rlog written 24 months ago by sjmonkley • 20 • updated 24 months ago by Michael Love ♦ 13k

votes

answer

696

views

answer

Dependence of rlog transformed value range on number of samples

deseq2 rlog written 2.4 years ago by snsansom • 10 • updated 2.4 years ago by Michael Love ♦ 13k

votes

answer

623

views

answer

Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2

deseq2 rlog variancestabilizingtransformation lfproc written 2.4 years ago by katja • 0 • updated 2.4 years ago by Michael Love ♦ 13k