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VST
•
reset
16
votes
12
replies
2.3k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
2.0 years ago
Joan Miró
▴ 80
7
votes
11
replies
4.9k
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
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
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
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
5
votes
2
replies
1.4k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 7.1 years ago by
Wolfgang Huber
★ 13k • written 7.1 years ago by
jiab
• 0
4
votes
6
replies
3.6k
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
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 5 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
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
4
votes
2
replies
1.6k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst
varianceStabilizingTransformation
DESeq2
3.5 years ago
Mia
▴ 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
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
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
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
2
replies
1.2k
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
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
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
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
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
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 2.6 years ago by
JB
▴ 10
2
votes
2
replies
834
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
1
vote
1
reply
759
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
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
1
vote
1
reply
1.0k
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
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
4
replies
1.7k
views
DESeq2 - VST data
DESeq2
VST
2.5 years ago
AP
• 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
2
replies
754
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
11 months ago
dwas
• 0
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
7.5 years ago
User34591
• 0
0
votes
1
reply
751
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
0
votes
1
reply
838
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
889
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
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
2
replies
1.4k
views
How to run vst transformation
RNASeqData
vst
updated 24 months ago by
Michael Love
41k • written 24 months ago by
sropri
• 0
0
votes
3
replies
1.1k
views
Using transformed matrix in DESeq2
DESeq2
VST
updated 3.3 years ago by
ATpoint
★ 4.1k • written 3.3 years ago by
Arun
• 0
0
votes
2
replies
806
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.1 years ago
vollkorrn
• 0
0
votes
1
reply
600
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
4
replies
2.9k
views
Normalization by variance stabilizing transformation VST
library
composition
vst
DESeq2
Normalization
2.4 years ago
kristoffersandas
• 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
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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