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vst
•
reset
3
votes
4
replies
481
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
8 weeks ago • updated 7 weeks ago
Eva
▴ 10
0
votes
2
replies
1.1k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
18 months ago
dwas
• 0
0
votes
1
reply
771
views
GSA type of input data
GSEA
GSA
vst
updated 23 months ago by
Michael Love
43k • written 23 months ago by
nhaus
▴ 70
1
vote
4
replies
2.4k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2
plotCounts
vst
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Laia
▴ 10
0
votes
2
replies
1.8k
views
How to run vst transformation
RNASeqData
vst
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
sropri
• 0
16
votes
12
replies
3.0k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
2.6 years ago
Joan Miró
▴ 80
0
votes
2
replies
1.0k
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
2.7 years ago
vollkorrn
• 0
1
vote
1
reply
986
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog
DESeq2
VST
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
BT
▴ 10
1
vote
2
replies
1.3k
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.9 years ago
Bex
• 0
1
vote
3
replies
1.8k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq
vst
R
rlog
DESeq2
updated 2.9 years ago by
Michael Love
43k • written 2.9 years ago by
celiburgos
• 0
4
votes
4
replies
2.7k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 12 months ago by
Gordon Smyth
52k • written 3.0 years ago by
mohammedtoufiq91
▴ 10
2
votes
1
reply
1.3k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST
Tumor-Purity
VST
DESeq2
Normalization
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Bioinf_sc
• 0
3
votes
5
replies
4.7k
views
Can I use VST on TPM data? (DESeq2)
DESeq2
VST
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
BT
▴ 10
0
votes
4
replies
3.7k
views
Normalization by variance stabilizing transformation VST
library
composition
vst
DESeq2
Normalization
3.0 years ago
kristoffersandas
• 0
1
vote
4
replies
2.2k
views
DESeq2 - VST data
DESeq2
VST
3.0 years ago
AP
• 0
2
votes
4
replies
3.3k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST
rlog
updated 2.9 years ago by
Sam
• 0 • written 3.1 years ago by
JB
▴ 10
3
votes
5
replies
1.9k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST
TCGATARGETGTEx
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
S
▴ 10
4
votes
9
replies
1.7k
views
Variance stabilising transformation to within given range
DESeq2
scaling
vst
updated 3.8 years ago by
Wolfgang Huber
★ 13k • written 3.8 years ago by
A
▴ 40
0
votes
3
replies
1.4k
views
Using transformed matrix in DESeq2
DESeq2
VST
updated 3.9 years ago by
ATpoint
★ 4.6k • written 3.9 years ago by
Arun
• 0
6
votes
6
replies
2.6k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2
VST
rsem
tximport
4.0 years ago
svlachavas
▴ 840
4
votes
2
replies
2.0k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst
varianceStabilizingTransformation
DESeq2
4.1 years ago
Mia
▴ 10
3
votes
2
replies
1.4k
views
Variance stabilized values and batch correction
deseq2
vst
updated 4.3 years ago by
Michael Love
43k • written 4.3 years ago by
le2336
▴ 20
2
votes
4
replies
9.5k
views
Deconvolution with CIBERSORT: input data
normalization
r
vst
cibersort
updated 4.3 years ago by
Kevin Blighe
★ 4.0k • written 4.3 years ago by
Matan G.
▴ 60
4
votes
5
replies
1.4k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2
vst
pca
cpm
4.8 years ago
svlachavas
▴ 840
0
votes
1
reply
3.4k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2
vst
rlog
updated 5.1 years ago by
Michael Love
43k • written 5.1 years ago by
juheon.maeng
• 0
0
votes
1
reply
1.1k
views
Using VST normalized values for "external" single gene analysis
VST
normalization
deseq2
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
filippo.martignano
• 0
4
votes
8
replies
24k
views
Variance stabilising transformation for machine learning
deseq2
vst
rna-seq
machine-learning
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
Manik Garg
▴ 20
2
votes
2
replies
970
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2
vst
covariates
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
Manik Garg
▴ 20
0
votes
1
reply
1.0k
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2
vst
variance
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
Bitao Qiu
• 0
1
vote
1
reply
1.2k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
filippo.martignano
• 0
0
votes
1
reply
895
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2
variancestabalizingtransformation
vst
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
chicoin1
• 0
4
votes
6
replies
4.0k
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 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
Marc Saric
▴ 70
6
votes
6
replies
8.4k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2
vst
rlog transformation
updated 5.9 years ago by
Wolfgang Huber
★ 13k • written 5.9 years ago by
salamandra
▴ 20
2
votes
3
replies
1.5k
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 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
agdif
▴ 10
7
votes
11
replies
5.4k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST
deseq2
boxplot
rnaseq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Konstantinos Yeles
▴ 80
2
votes
6
replies
2.6k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA
VST
7.4 years ago • updated 7.1 years ago
harelarik
▴ 60
5
votes
2
replies
1.6k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 7.7 years ago by
Wolfgang Huber
★ 13k • written 7.7 years ago by
jiab
• 0
0
votes
6
replies
1.9k
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
8.1 years ago
User34591
• 0
6
votes
4
replies
4.1k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2
rlog transformation
vst
variancestabilizingtransformation
rlog
updated 8.3 years ago by
Michael Love
43k • written 8.3 years ago by
longwoodSequencer
• 0
0
votes
4
replies
1.4k
views
rlog fast=TRUE not correct?
deseq2
rlog transformation
vst
8.5 years ago
ldetorrente
▴ 10
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Comment: Can't post a question?
by
Aimee
• 0
I copied my text to a file in linux and ran: ```r grep --color='auto' -P -n "[^\x00-\x7F]" filename.txt ``` It highlighted everything that…
Answer: sva: get a sv for RIN scores
by
Gordon Smyth
52k
Surrogate variables are not constructed from known variates, so one doesn't get surrogate variables for RIN scores. I am guessing that the …
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by
alexandra.casey
• 0
any update? It's still not working for me. I'm amazed it's taking this long to fix!
Comment: git push errors
by
Jiping Wang
▴ 90
I have bioconductor remote named "upstream". thanks for help!! I missed ":devel" after master. ``` (base) jon@Jipings-2021-macbook-pro Rib…
Answer: git push errors
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67k
This is a question for the bioc-devel listserv (bioc-devel@r-project.org) rather than the support site. However, it looks like you are s…
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Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
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