Showing : vst • reset
0
votes
2
replies
724
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
588
views
GSA type of input data
GSEA GSA vst
updated 15 months ago by 41k • written 15 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 17 months ago by 41k • written 17 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
24 months ago Joan Miró ▴ 80
0
votes
2
replies
787
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
2.1 years ago vollkorrn • 0
1
vote
1
reply
739
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 2.2 years ago by 41k • written 2.2 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
1.4k
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
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
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 2.3 years ago by 41k • written 2.3 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
2
votes
4
replies
2.4k
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
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
7.9k
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
2.6k
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
874
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
823
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
826
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
0
votes
1
reply
735
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
1
vote
1
reply
985
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 5.0 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
6.7 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
1.6k
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
1.2k
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
7.8 years ago ldetorrente ▴ 10
39 results • Page 1 of 1
Recent ...
Replies
Answer: rlog transformation by Michael Love 41k
It is dependent on the other samples in the dataset.
Answer: ONT long-read RNA sequencing - data analysis options by Michael Love 41k
*"This worked really well for brain but has not work as well for lung as I get #N/A for many padj"* See the vignette for the cause of th…
Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by Michael Love 41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values by Michael Love 41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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