Showing : vst • reset
4
votes
8
replies
11k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 2.8 years ago by 37k • written 2.8 years ago by ▴ 20
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
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 37k • written 4.0 years ago by ▴ 70
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
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 37k • written 5.8 years ago by • 0
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 37k • written 3.2 years ago by ▴ 70
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
0
votes
1
reply
1.2k
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 37k • written 2.6 years ago by • 0
2
votes
5
replies
1.1k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 5 months ago by 37k • written 5 months ago by ▴ 10
0
votes
6
replies
994
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
5.6 years ago User34591 • 0
5
votes
2
replies
968
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
5
votes
6
replies
905
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
18 months ago • updated 17 months ago svlachavas ▴ 780
2
votes
3
replies
821
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 37k • written 4.0 years ago by • 0
0
votes
4
replies
764
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
5.9 years ago ldetorrente ▴ 10
4
votes
9
replies
569
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 15 months ago by 13k • written 15 months ago by ▴ 40
3
votes
2
replies
547
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
18 months ago Mia ▴ 10
3
votes
5
replies
529
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 8 months ago by 37k • written 8 months ago by ▴ 10
1
vote
1
reply
504
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 3.1 years ago by 37k • written 3.2 years ago by • 0
0
votes
4
replies
504
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
5 months ago kristoffersandas • 0
0
votes
3
replies
481
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
415
views
Variance stabilized values and batch correction
deseq2 vst
updated 21 months ago by 37k • written 21 months ago by ▴ 20
2
votes
4
replies
413
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
4
votes
5
replies
388
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
2.3 years ago svlachavas ▴ 780
1
vote
4
replies
386
views
DESeq2 - VST data
DESeq2 VST
6 months ago AP • 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 37k • written 2.9 years ago by ▴ 20
0
votes
12
replies
361
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
4 weeks ago • updated 25 days ago Joan Miró • 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 37k • written 3.0 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 37k • written 3.2 years ago by • 0
0
votes
1
reply
321
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 2.8 years ago by 37k • written 2.8 years ago by • 0
1
vote
3
replies
296
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 4 months ago by 37k • written 4 months ago by • 0
3
votes
2
replies
288
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
5 months ago mohammedtoufiq91 ▴ 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 37k • written 5 months ago by • 0
1
vote
2
replies
230
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
4 months ago Bex • 0
0
votes
1
reply
150
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 4 months ago by 37k • written 4 months ago by ▴ 10
0
votes
2
replies
131
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
8 weeks ago • updated 7 weeks ago vollkorrn • 0
0
votes
2
replies
119
views
How to run vst transformation
RNASeqData vst
updated 12 days ago by 37k • written 18 days ago by • 0
36 results • Page 1 of 1
Recent ...
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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