Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
VST
•
reset
0
votes
2
replies
738
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
10 months ago
dwas
• 0
0
votes
1
reply
594
views
GSA type of input data
GSEA
GSA
vst
updated 16 months ago by
Michael Love
41k • written 16 months ago by
nhaus
▴ 30
1
vote
4
replies
1.6k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2
plotCounts
vst
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Laia
▴ 10
0
votes
2
replies
1.4k
views
How to run vst transformation
RNASeqData
vst
updated 23 months ago by
Michael Love
41k • written 24 months ago by
sropri
• 0
16
votes
12
replies
2.3k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
2.0 years ago • updated 24 months ago
Joan Miró
▴ 80
0
votes
2
replies
797
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.1 years ago
vollkorrn
• 0
1
vote
1
reply
750
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
BT
▴ 10
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.3 years ago
Bex
• 0
1
vote
3
replies
1.5k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
celiburgos
• 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 4 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
2
votes
1
reply
1.0k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST
Tumor-Purity
VST
DESeq2
Normalization
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
Bioinf_sc
• 0
3
votes
5
replies
3.8k
views
Can I use VST on TPM data? (DESeq2)
DESeq2
VST
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
BT
▴ 10
0
votes
4
replies
2.8k
views
Normalization by variance stabilizing transformation VST
library
composition
vst
DESeq2
Normalization
2.4 years ago
kristoffersandas
• 0
1
vote
4
replies
1.7k
views
DESeq2 - VST data
DESeq2
VST
2.4 years ago
AP
• 0
2
votes
4
replies
2.5k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.3 years ago by
Sam
• 0 • written 2.5 years ago by
JB
▴ 10
3
votes
5
replies
1.5k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST
TCGATARGETGTEx
DESeq2
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
S
▴ 10
4
votes
9
replies
1.4k
views
Variance stabilising transformation to within given range
DESeq2
scaling
vst
updated 3.2 years ago by
Wolfgang Huber
★ 13k • written 3.2 years ago by
A
▴ 40
0
votes
3
replies
1.1k
views
Using transformed matrix in DESeq2
DESeq2
VST
updated 3.3 years ago by
ATpoint
★ 4.0k • written 3.3 years ago by
Arun
• 0
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
3.4 years ago
svlachavas
▴ 830
4
votes
2
replies
1.6k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst
varianceStabilizingTransformation
DESeq2
3.4 years ago
Mia
▴ 10
3
votes
2
replies
1.1k
views
Variance stabilized values and batch correction
deseq2
vst
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
le2336
▴ 20
2
votes
4
replies
8.0k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Matan G.
▴ 60
4
votes
5
replies
1.1k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
4.2 years ago
svlachavas
▴ 830
0
votes
1
reply
2.7k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
juheon.maeng
• 0
0
votes
1
reply
877
views
Using VST normalized values for "external" single gene analysis
VST
normalization
deseq2
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
filippo.martignano
• 0
4
votes
8
replies
22k
views
Variance stabilising transformation for machine learning
deseq2
vst
rna-seq
machine-learning
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
Manik Garg
▴ 20
2
votes
2
replies
833
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Manik Garg
▴ 20
0
votes
1
reply
833
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2
vst
variance
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Bitao Qiu
• 0
0
votes
1
reply
745
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2
variancestabalizingtransformation
vst
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
chicoin1
• 0
1
vote
1
reply
998
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
filippo.martignano
• 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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
Marc Saric
▴ 70
6
votes
6
replies
7.7k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2
vst
rlog transformation
updated 5.3 years ago by
Wolfgang Huber
★ 13k • written 5.3 years ago by
salamandra
▴ 20
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 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
agdif
▴ 10
7
votes
11
replies
4.8k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST
deseq2
boxplot
rnaseq
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
Konstantinos Yeles
▴ 80
2
votes
6
replies
2.2k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA
VST
6.8 years ago • updated 6.5 years ago
harelarik
▴ 60
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
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.5 years ago
User34591
• 0
6
votes
4
replies
3.7k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
longwoodSequencer
• 0
0
votes
4
replies
1.3k
views
rlog fast=TRUE not correct?
deseq2
rlog transformation
vst
7.9 years ago
ldetorrente
▴ 10
39 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
• 0
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Awards
• All
Popular Question
to
James W. MacDonald
65k
Scholar
to
Michael Love
41k
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Locations
• All
United States,
just now
France,
3 minutes ago
Sweden,
6 minutes ago
The Netherlands,
7 minutes ago
Sweden,
8 minutes ago
Traffic: 1128 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6