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VST
•
reset
16
votes
12
replies
2.2k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
23 months ago
Joan Miró
▴ 80
7
votes
11
replies
4.7k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST
deseq2
boxplot
rnaseq
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
Konstantinos Yeles
▴ 80
6
votes
4
replies
3.6k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
longwoodSequencer
• 0
6
votes
6
replies
7.6k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2
vst
rlog transformation
updated 5.2 years ago by
Wolfgang Huber
★ 13k • written 5.2 years ago by
salamandra
▴ 20
6
votes
6
replies
2.3k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2
VST
rsem
tximport
3.3 years ago
svlachavas
▴ 830
5
votes
2
replies
1.4k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 7.0 years ago by
Wolfgang Huber
★ 13k • written 7.0 years ago by
jiab
• 0
4
votes
6
replies
3.5k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2
normalization
rna-seq
TCGA
vst
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Marc Saric
▴ 70
4
votes
4
replies
1.9k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 3 months ago by
Gordon Smyth
50k • written 2.3 years ago by
mohammedtoufiq91
▴ 10
4
votes
8
replies
21k
views
Variance stabilising transformation for machine learning
deseq2
vst
rna-seq
machine-learning
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
Manik Garg
▴ 20
4
votes
2
replies
1.5k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst
varianceStabilizingTransformation
DESeq2
3.4 years ago
Mia
▴ 10
4
votes
9
replies
1.4k
views
Variance stabilising transformation to within given range
DESeq2
scaling
vst
updated 3.1 years ago by
Wolfgang Huber
★ 13k • written 3.1 years ago by
A
▴ 40
4
votes
5
replies
1.0k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
4.1 years ago
svlachavas
▴ 830
3
votes
5
replies
1.5k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST
TCGATARGETGTEx
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
S
▴ 10
3
votes
5
replies
3.7k
views
Can I use VST on TPM data? (DESeq2)
DESeq2
VST
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
BT
▴ 10
3
votes
2
replies
1.1k
views
Variance stabilized values and batch correction
deseq2
vst
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
le2336
▴ 20
2
votes
6
replies
2.1k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA
VST
6.7 years ago • updated 6.4 years ago
harelarik
▴ 60
2
votes
4
replies
7.7k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Matan G.
▴ 50
2
votes
3
replies
1.3k
views
Better to use rlog or vst transformation for data quality assessment of differental expression data based on size factors?
DESeq2
quality assesment
vst
rlog transformation
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
agdif
▴ 10
2
votes
1
reply
982
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST
Tumor-Purity
VST
DESeq2
Normalization
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
Bioinf_sc
• 0
2
votes
4
replies
2.4k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.2 years ago by
Sam
• 0 • written 2.5 years ago by
JB
▴ 10
2
votes
2
replies
810
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Manik Garg
▴ 20
1
vote
1
reply
713
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
BT
▴ 10
1
vote
3
replies
1.4k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
celiburgos
• 0
1
vote
1
reply
956
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
filippo.martignano
• 0
1
vote
2
replies
990
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.2 years ago
Bex
• 0
1
vote
4
replies
1.6k
views
DESeq2 - VST data
DESeq2
VST
2.4 years ago
AP
• 0
1
vote
4
replies
1.5k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2
plotCounts
vst
updated 17 months ago by
Michael Love
41k • written 17 months ago by
Laia
▴ 10
0
votes
2
replies
692
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
10 months ago
dwas
• 0
0
votes
6
replies
1.6k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.4 years ago
User34591
• 0
0
votes
1
reply
722
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2
variancestabalizingtransformation
vst
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
chicoin1
• 0
0
votes
1
reply
804
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2
vst
variance
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Bitao Qiu
• 0
0
votes
1
reply
849
views
Using VST normalized values for "external" single gene analysis
VST
normalization
deseq2
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
filippo.martignano
• 0
0
votes
1
reply
2.6k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
juheon.maeng
• 0
0
votes
2
replies
1.3k
views
How to run vst transformation
RNASeqData
vst
updated 22 months ago by
Michael Love
41k • written 23 months ago by
sropri
• 0
0
votes
3
replies
1.1k
views
Using transformed matrix in DESeq2
DESeq2
VST
updated 3.2 years ago by
ATpoint
★ 4.0k • written 3.2 years ago by
Arun
• 0
0
votes
2
replies
768
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.0 years ago • updated 24 months ago
vollkorrn
• 0
0
votes
1
reply
556
views
GSA type of input data
GSEA
GSA
vst
updated 15 months ago by
Michael Love
41k • written 15 months ago by
nhaus
▴ 10
0
votes
4
replies
2.7k
views
Normalization by variance stabilizing transformation VST
library
composition
vst
DESeq2
Normalization
2.3 years ago
kristoffersandas
• 0
0
votes
4
replies
1.2k
views
rlog fast=TRUE not correct?
deseq2
rlog transformation
vst
7.8 years ago
ldetorrente
▴ 10
39 results • Page
1 of 1
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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