Showing : VST • reset
0
votes
2
replies
400
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
4 months ago dwas • 0
0
votes
1
reply
381
views
GSA type of input data
GSEA GSA vst
updated 9 months ago by 40k • written 9 months ago by • 0
1
vote
4
replies
953
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2 plotCounts vst
updated 11 months ago by 40k • written 11 months ago by ▴ 10
0
votes
2
replies
1.1k
views
How to run vst transformation
RNASeqData vst
updated 16 months ago by 40k • written 17 months ago by • 0
0
votes
12
replies
1.7k
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
17 months ago Joan Miró • 0
0
votes
2
replies
611
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
18 months ago vollkorrn • 0
1
vote
1
reply
539
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 20 months ago by 40k • written 20 months ago by ▴ 10
1
vote
2
replies
740
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
20 months ago Bex • 0
1
vote
3
replies
1.1k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 20 months ago by 40k • written 21 months ago by • 0
3
votes
3
replies
1.3k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
written 21 months ago by ▴ 10
2
votes
1
reply
796
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 21 months ago by 40k • written 21 months ago by • 0
3
votes
5
replies
3.0k
views
Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 22 months ago by 40k • written 22 months ago by ▴ 10
0
votes
4
replies
2.1k
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
22 months ago kristoffersandas • 0
1
vote
4
replies
1.2k
views
DESeq2 - VST data
DESeq2 VST
22 months ago AP • 0
2
votes
4
replies
1.7k
views
Is it valid to do gene comparisons on VST or rlog transformed data?
VST rlog
updated 20 months ago by • 0 • written 23 months ago by ▴ 10
3
votes
5
replies
1.2k
views
VST transformation and covariates in the TCGA TARGET GTEx dataset
VST TCGATARGETGTEx DESeq2
updated 2.0 years ago by 40k • written 2.0 years ago by ▴ 10
4
votes
9
replies
1.2k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 2.6 years ago by 13k • written 2.7 years ago by ▴ 40
0
votes
3
replies
881
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
6
votes
6
replies
2.0k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
2.8 years ago svlachavas ▴ 810
3
votes
2
replies
1.2k
views
VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
2.9 years ago Mia ▴ 10
3
votes
2
replies
880
views
Variance stabilized values and batch correction
deseq2 vst
updated 3.1 years ago by 40k • written 3.1 years ago by ▴ 20
2
votes
4
replies
6.6k
views
Deconvolution with CIBERSORT: input data
normalization r vst cibersort
updated 3.2 years ago by 3.8k • written 3.2 years ago by ▴ 50
4
votes
5
replies
820
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
3.6 years ago svlachavas ▴ 810
0
votes
1
reply
2.2k
views
DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per million?
deseq2 vst rlog
updated 3.9 years ago by 40k • written 3.9 years ago by • 0
0
votes
1
reply
724
views
Using VST normalized values for "external" single gene analysis
VST normalization deseq2
updated 4.1 years ago by 40k • written 4.1 years ago by • 0
4
votes
8
replies
20k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 4.1 years ago by 40k • written 4.1 years ago by ▴ 20
2
votes
2
replies
660
views
Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
deseq2 vst covariates
updated 4.3 years ago by 40k • written 4.3 years ago by ▴ 20
0
votes
1
reply
667
views
Comparing transcriptome variation across groups after Variance stabilizing transformation using DESeq2
deseq2 vst variance
updated 4.3 years ago by 40k • written 4.3 years ago by • 0
1
vote
1
reply
814
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 4.5 years ago by 40k • written 4.5 years ago by • 0
0
votes
1
reply
602
views
Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 4.5 years ago by 40k • written 4.5 years ago by • 0
4
votes
6
replies
3.1k
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 4.6 years ago by 40k • written 4.6 years ago by ▴ 70
6
votes
6
replies
7.0k
views
DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
deseq2 vst rlog transformation
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 20
2
votes
3
replies
1.1k
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 5.3 years ago by 40k • written 5.3 years ago by ▴ 10
7
votes
11
replies
4.2k
views
Comparing means of VST tranformed RNA-Seq counts in different groups of samples with boxplots
VST deseq2 boxplot rnaseq
updated 5.3 years ago by 40k • written 5.4 years ago by ▴ 80
2
votes
6
replies
1.9k
views
Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
LIMMA VST
6.2 years ago • updated 5.9 years ago harelarik ▴ 60
5
votes
2
replies
1.3k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 6.5 years ago by 13k • written 6.5 years ago by • 0
0
votes
6
replies
1.5k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
6.9 years ago User34591 • 0
6
votes
4
replies
3.3k
views
regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 7.2 years ago by 40k • written 7.2 years ago by • 0
0
votes
4
replies
1.1k
views
rlog fast=TRUE not correct?
deseq2 rlog transformation vst
7.3 years ago ldetorrente ▴ 10
39 results • Page 1 of 1
Recent ...
Replies
Answer: Gviz: UcscTrack and "GC Percent" information by Daniel E. Weeks ▴ 20
**Answer** In https://github.com/ivanek/Gviz/issues/71 an update that fixes this issue was documented - there it is stated that "…
Comment: Biostrings error at retrieving protein sequences by James W. MacDonald 63k
It depends on what kind of whitespace it is. If the whitespace is just a space, then it will work. But if it's a tab, it won't. ``` > gsub…
Comment: Biostrings error at retrieving protein sequences by nromerov • 0
If i write it like ```r gsub(" .*", "", names(protein_sequences)) ``` it will delet all the extra information if it is on the AAString…
Comment: bug in block.plsda from mixOmics? by Lluís Revilla Sancho ▴ 720
Oh, sorry for the noise, I see that just after Bioconductor 3.16 the bug is fixed in both 3.17 and in devel. Thanks for checking.
Answer: Mixed up sample info with plotPCA by Michael Love 40k
I can already tell there is code you aren't showing. For example, your `pcaData` has a variable 'group' that isn't in the previous sample i…
Votes
Answer: Mouse to Human Genes using bioconductor
Mouse to Human Genes using bioconductor
Answer: Biostrings error at retrieving protein sequences
Answer: Biostrings error at retrieving protein sequences
Answer: How do I merge a list of GRanges?
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