Showing : vst • reset
0
votes
12
replies
345
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
4 weeks ago • updated 22 days ago Joan Miró • 0
7
votes
11
replies
2.9k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST deseq2 boxplot rnaseq
updated 4.0 years ago by 36k • written 4.0 years ago by ▴ 70
4
votes
9
replies
565
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 15 months ago by 13k • written 15 months ago by ▴ 40
4
votes
8
replies
11k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 2.8 years ago by 36k • written 2.8 years ago by ▴ 20
1
vote
6
replies
1.3k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA VST
4.8 years ago • updated 4.6 years ago harelarik ▴ 50
6
votes
6
replies
3.7k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2 vst rlog transformation
updated 3.4 years ago by 13k • written 3.4 years ago by ▴ 20
4
votes
6
replies
2.2k
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 3.2 years ago by 36k • written 3.2 years ago by ▴ 70
5
votes
6
replies
895
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
17 months ago svlachavas ▴ 780
0
votes
6
replies
991
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
5.6 years ago User34591 • 0
4
votes
5
replies
386
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
2.2 years ago svlachavas ▴ 780
2
votes
5
replies
1.1k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 5 months ago by 36k • written 5 months ago by ▴ 10
3
votes
5
replies
526
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 7 months ago by 36k • written 8 months ago by ▴ 10
2
votes
4
replies
2.8k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 21 months ago by 3.5k • written 21 months ago by ▴ 40
0
votes
4
replies
763
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
5.9 years ago ldetorrente ▴ 10
6
votes
4
replies
2.5k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 5.8 years ago by 36k • written 5.8 years ago by • 0
1
vote
4
replies
383
views
DESeq2 - VST data
DESeq2 VST
6 months ago AP • 0
0
votes
4
replies
496
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
5 months ago kristoffersandas • 0
2
votes
4
replies
412
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 4 months ago by • 0 • written 7 months ago by ▴ 10
1
vote
3
replies
293
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 4 months ago by 36k • written 4 months ago by • 0
2
votes
3
replies
819
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 4.0 years ago by 36k • written 4.0 years ago by • 0
0
votes
3
replies
478
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 16 months ago by ★ 1.2k • written 16 months ago by • 0
3
votes
2
replies
545
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
18 months ago Mia ▴ 10
5
votes
2
replies
967
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 5.1 years ago by 13k • written 5.1 years ago by • 0
3
votes
2
replies
411
views
Variance stabilized values and batch correction
deseq2 vst
updated 21 months ago by 36k • written 21 months ago by ▴ 20
0
votes
2
replies
130
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
7 weeks ago vollkorrn • 0
1
vote
2
replies
230
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
4 months ago Bex • 0
2
votes
2
replies
369
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 2.9 years ago by 36k • written 2.9 years ago by ▴ 20
3
votes
2
replies
286
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
5 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
117
views
How to run vst transformation
RNASeqData vst
updated 9 days ago by 36k • written 14 days ago by • 0
0
votes
1
reply
149
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 4 months ago by 36k • written 4 months ago by ▴ 10
2
votes
1
reply
262
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 5 months ago by 36k • written 5 months ago by • 0
0
votes
1
reply
1.1k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 2.6 years ago by 36k • written 2.6 years ago by • 0
0
votes
1
reply
338
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 3.0 years ago by 36k • written 3.0 years ago by • 0
1
vote
1
reply
501
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 3.1 years ago by 36k • written 3.2 years ago by • 0
0
votes
1
reply
319
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 2.8 years ago by 36k • written 2.8 years ago by • 0
0
votes
1
reply
325
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 3.2 years ago by 36k • written 3.2 years ago by • 0
36 results • Page 1 of 1
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Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Hi Michael, thanks for your reply. One more question. If the qvalue (and pvalue) for all DTEs are the same, the Volcano plot will look lik…
Comment: R: problem with running time-series analysis software: Mfuzz by soda ▴ 80
I have solved this problem by myself. My data.frame is not suitable for Mfuzz.
Comment: R: problem with running time-series analysis software: Mfuzz by Kevin Blighe 3.5k
Cross-posted: https://www.biostars.org/p/9524023/
Comment: ROC plot for OPLS-DA by Eddie • 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
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