Showing : vst • reset
3
votes
4
replies
439
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
4 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
17 months ago dwas • 0
0
votes
1
reply
753
views
GSA type of input data
GSEA GSA vst
updated 22 months ago by 42k • written 22 months ago by ▴ 70
1
vote
4
replies
2.3k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2 plotCounts vst
updated 2.1 years ago by 42k • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.8k
views
How to run vst transformation
RNASeqData vst
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
16
votes
12
replies
2.9k
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
2.6 years ago vollkorrn • 0
1
vote
1
reply
969
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 2.8 years ago by 42k • written 2.8 years ago by ▴ 10
1
vote
2
replies
1.3k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
2.8 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 2.8 years ago by 42k • written 2.8 years ago by • 0
4
votes
4
replies
2.7k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 11 months ago by 51k • written 2.9 years ago by ▴ 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 2.9 years ago by 42k • written 2.9 years ago by • 0
3
votes
5
replies
4.6k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 2.9 years ago by 42k • written 3.0 years ago by ▴ 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
2.1k
views
DESeq2 - VST data
DESeq2 VST
3.0 years ago AP • 0
2
votes
4
replies
3.2k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 2.8 years ago by • 0 • written 3.1 years ago by ▴ 10
3
votes
5
replies
1.9k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 3.1 years ago by 42k • written 3.2 years ago by ▴ 10
4
votes
9
replies
1.6k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 3.7 years ago by ★ 13k • written 3.8 years ago by ▴ 40
0
votes
3
replies
1.4k
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 3.9 years ago by ★ 4.5k • written 3.9 years ago by • 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 ▴ 830
4
votes
2
replies
2.0k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
4.0 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 42k • written 4.3 years ago by ▴ 20
2
votes
4
replies
9.4k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 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
4.7 years ago svlachavas ▴ 830
0
votes
1
reply
3.3k
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 42k • written 5.1 years ago by • 0
0
votes
1
reply
1.1k
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 5.2 years ago by 42k • written 5.2 years ago by • 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 42k • written 5.3 years ago by ▴ 20
2
votes
2
replies
963
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 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 42k • written 5.5 years ago by • 0
1
vote
1
reply
1.2k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
votes
1
reply
883
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 5.6 years ago by 42k • written 5.6 years ago by • 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 5.7 years ago by 42k • written 5.7 years ago by ▴ 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 ★ 13k • written 5.9 years ago by ▴ 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 6.4 years ago by 42k • written 6.4 years ago by ▴ 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 42k • written 6.5 years ago by ▴ 80
2
votes
6
replies
2.5k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA VST
7.3 years ago • updated 7.0 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 7.6 years ago by ★ 13k • written 7.6 years ago by • 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 42k • written 8.3 years ago by • 0
0
votes
4
replies
1.4k
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
8.4 years ago ldetorrente ▴ 10
40 results • Page 1 of 1
Recent ...
Replies
Comment: Appropriate ways to filter counts data for voom/limma by dorothylminter • 0
The proper way to filter count data for voom/limma emphasizes the importance of choosing the right filtering technique to enhance detection…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
Awards • All
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Michael Stadler ▴ 350
Scholar to ATpoint ★ 4.5k
Commentator to James W. MacDonald 67k
Popular Question to Stefano Mangiola ▴ 20
Locations • All
Belgium, just now
Seattle, WA, United States, 3 minutes ago
Poland, 16 minutes ago
France, 29 minutes ago
Japan, 31 minutes ago
Traffic: 818 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