Showing : VST • reset
3
votes
4
replies
734
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
5 months ago Eva ▴ 10
0
votes
2
replies
1.3k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
21 months ago dwas • 0
0
votes
1
reply
850
views
GSA type of input data
GSEA GSA vst
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 70
1
vote
4
replies
2.8k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2 plotCounts vst
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
votes
2
replies
1.9k
views
How to run vst transformation
RNASeqData vst
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
16
votes
12
replies
3.3k
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
2.9 years ago Joan Miró ▴ 80
0
votes
2
replies
1.1k
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
3.0 years ago vollkorrn • 0
1
vote
1
reply
1.1k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 10
1
vote
2
replies
1.4k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
3.2 years ago Bex • 0
1
vote
3
replies
2.0k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
4
votes
4
replies
3.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 15 months ago by 52k • written 3.2 years ago by ▴ 10
2
votes
1
reply
1.4k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
3
votes
5
replies
5.1k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
4
replies
4.3k
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
3.3 years ago kristoffersandas • 0
1
vote
4
replies
2.4k
views
DESeq2 - VST data
DESeq2 VST
3.3 years ago AP • 0
2
votes
4
replies
3.7k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 3.2 years ago by • 0 • written 3.4 years ago by ▴ 10
3
votes
5
replies
2.1k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
4
votes
9
replies
1.8k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 4.1 years ago by ★ 13k • written 4.1 years ago by ▴ 40
0
votes
3
replies
1.6k
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 4.2 years ago by ★ 4.7k • written 4.2 years ago by • 0
6
votes
6
replies
2.7k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.3 years ago svlachavas ▴ 840
4
votes
2
replies
2.2k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
4.3 years ago Mia ▴ 10
3
votes
2
replies
1.6k
views
Variance stabilized values and batch correction
deseq2 vst
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 20
2
votes
4
replies
10k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 60
4
votes
5
replies
1.5k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
5.1 years ago svlachavas ▴ 840
0
votes
1
reply
3.7k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
1
reply
1.2k
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
4
votes
8
replies
25k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
2
votes
2
replies
1.0k
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
1
reply
1.3k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
970
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
4
votes
6
replies
4.2k
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 6.1 years ago by 43k • written 6.1 years ago by ▴ 70
6
votes
6
replies
8.7k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2 vst rlog transformation
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 20
2
votes
3
replies
1.6k
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 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
7
votes
11
replies
5.7k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST deseq2 boxplot rnaseq
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 80
2
votes
6
replies
2.7k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA VST
7.6 years ago • updated 7.4 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 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
0
votes
6
replies
2.1k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
8.4 years ago User34591 • 0
6
votes
4
replies
4.3k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
4
replies
1.5k
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
8.8 years ago ldetorrente ▴ 10
40 results • Page 1 of 1
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Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Comment: deseq2 lfc shrinkage with few DEGs by Robert • 0
I'm dealing with a similar situation. I assume the coefficients related to batch effect would need to be included in idx also, is this corr…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Thank you so much!! Yeah I had thought about this too, regarding the fact that DiffBind is a wrapper for counting peaks in this way in R di…
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by aitor • 0
Hi everyone. I have a RIP-Seq analysis with 3 conditions and 3 assays (IP, IgG and Input for each of them). 4 replicates for each conditio…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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