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
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
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
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
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
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
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
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
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
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.5 years ago
User34591
• 0
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
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
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
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
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
1.6k
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
4
replies
1.3k
views
rlog fast=TRUE not correct?
deseq2
rlog transformation
vst
7.9 years ago
ldetorrente
▴ 10
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
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
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
1
vote
3
replies
1.4k
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
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
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
0
votes
2
replies
733
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
10 months ago
dwas
• 0
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
2
votes
2
replies
830
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
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
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
0
votes
2
replies
1.4k
views
How to run vst transformation
RNASeqData
vst
updated 23 months ago by
Michael Love
41k • written 23 months ago by
sropri
• 0
0
votes
2
replies
793
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.1 years ago
vollkorrn
• 0
1
vote
2
replies
1.0k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.3 years ago
Bex
• 0
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
1
vote
1
reply
748
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
0
votes
1
reply
591
views
GSA type of input data
GSEA
GSA
vst
updated 16 months ago by
Michael Love
41k • written 16 months ago by
nhaus
▴ 30
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
0
votes
1
reply
829
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
743
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
996
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
39 results • Page
1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
Awards
• All
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Locations
• All
Japan,
just now
South Korea,
just now
Singapore,
just now
Uganda,
6 minutes ago
Belgium,
9 minutes ago
Traffic: 796 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