Showing : VST • reset
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.4 years ago by ▴ 10
0
votes
2
replies
734
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
591
views
GSA type of input data
GSEA GSA vst
updated 16 months ago by 41k • written 16 months ago by ▴ 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 41k • written 18 months ago by ▴ 10
0
votes
2
replies
1.4k
views
How to run vst transformation
RNASeqData vst
updated 23 months ago by 41k • written 23 months ago by • 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
795
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
2.1 years ago vollkorrn • 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 41k • written 2.3 years ago by ▴ 10
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 • 0 • written 2.5 years ago by ▴ 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 41k • written 2.3 years ago by • 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 41k • written 2.4 years ago by • 0
3
votes
5
replies
3.8k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 2.4 years ago by 41k • written 2.4 years ago by ▴ 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
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 41k • written 2.6 years ago by ▴ 10
4
votes
9
replies
1.4k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 3.2 years ago by ★ 13k • written 3.2 years ago by ▴ 40
0
votes
3
replies
1.1k
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 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 41k • written 3.7 years ago by ▴ 20
2
votes
4
replies
8.0k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 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 41k • written 4.5 years ago by • 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 41k • written 4.7 years ago by • 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 41k • written 4.7 years ago by ▴ 20
2
votes
2
replies
831
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 20
0
votes
1
reply
830
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 4.9 years ago by 41k • written 4.9 years ago by • 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 41k • written 5.1 years ago by • 0
0
votes
1
reply
744
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 5.1 years ago by 41k • written 5.1 years ago by • 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 41k • written 5.2 years ago by ▴ 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 ★ 13k • written 5.3 years ago by ▴ 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 41k • written 5.9 years ago by ▴ 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 41k • written 5.9 years ago by ▴ 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 ★ 13k • written 7.0 years ago by • 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 41k • written 7.7 years ago by • 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: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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