Showing : variancestabilizingtransformation • reset
7
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6
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11k
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DESEq2 VST error
deseq2 variancestabilizingtransformation
updated 13 months ago by • 0 • written 6.2 years ago by ▴ 40
3
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2
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1.2k
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VST Failing Error in estimateDispersionsFit(object, quiet = TRUE, fitType)
vst varianceStabilizingTransformation DESeq2
2.9 years ago Mia ▴ 10
0
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3
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2.3k
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Data normalization and transformation using DESeq2
deseq2 normalization rnaseq rlog transformation variancestabilizingtransformation
4.8 years ago chiara.facciotto • 0
4
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4
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2.2k
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Applying varianceStabilizingTransformation to log transformed RNA seq data from cBioPortal
variancestabilizingtransformation rnaseq cBioPortal deseq2
updated 5.3 years ago by ▴ 20 • written 5.3 years ago by • 0
6
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14
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2.5k
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Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 5.4 years ago by 13k • written 5.4 years ago by ▴ 810
2
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1
reply
3.5k
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choosing the normalization method (rlog, variance stabilizing transformation)
variancestabilizingtransformation rlog transformation deseq2
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 80
1
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2
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1.2k
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an unexplained phenomenon using variance stabilizing transformation for downstream analysis
variancestabilizingtransformation normalization
5.8 years ago lirongrossmann ▴ 80
0
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1
reply
983
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Distribution of transformed data using VST
variancestabilizingtransformation deseq2
updated 5.9 years ago by 40k • written 5.9 years ago by ▴ 80
2
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5
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1.2k
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calculating logfold change from variance stabilizing transformation
deseq2 logfoldchange variancestabilizingtransformation
updated 5.9 years ago by 40k • written 5.9 years ago by ▴ 80
1
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4
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1.4k
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expression matrix with varianceStabilizingTransformation
deseq2 variancestabilizingtransformation rnaseq
updated 5.9 years ago by 40k • written 6.0 years ago by ▴ 80
0
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6
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2.7k
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Different PCA plots using rlog and vsd on the same data set
deseq2 rlog variancestabilizingtransformation plotpca pca
6.0 years ago lirongrossmann ▴ 80
0
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3
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1.9k
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deseq2 vst transformation
deseq2 variancestabilizingtransformation
updated 6.0 years ago by 40k • written 6.0 years ago by • 0
1
vote
1
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3.1k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
6.5 years ago stats134711 • 0
3
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8
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3.1k
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Using DESeq2 with Nanostring data (for VST only)
deseq2 variancestabilizingtransformation nanostring
updated 6.5 years ago by 40k • written 6.5 years ago by ▴ 10
2
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2
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2.4k
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DESeq2: Difference in rlog and vst values if run transform before or after running DESeq
deseq2 rlog variancestabilizingtransformation DESeq
updated 6.6 years ago by 40k • written 6.6 years ago by ▴ 10
3
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6
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4.5k
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[DESEQ2] VST with rlog + normalization (size factor estimation) for downstream (clustering) analysis.
deseq2 normalization variancestabilizingtransformation
updated 7.1 years ago by • 0 • written 8.4 years ago by ▴ 120
6
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4
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3.3k
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regularized log transformation- loss of zero values for sparsely expressed genes
deseq2 rlog transformation vst variancestabilizingtransformation rlog
updated 7.1 years ago by 40k • written 7.1 years ago by • 0
2
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7
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2.1k
views
DESEQ2 VST sample number limits?
deseq2 variancestabilizingtransformation limits size
7.2 years ago b.cox • 0
3
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3
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3.8k
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How to do a confounding variable adjustment without using the treatment information?
deseq2 rnaseq_analysis variancestabilizingtransformation confounders
updated 7.3 years ago by 40k • written 7.3 years ago by ▴ 10
2
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2
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2.8k
views
DESeq2 transformation to use for PCA plot
deseq2 pca rlog transformation variancestabilizingtransformation
7.4 years ago Shobana Sekar ▴ 20
1
vote
3
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1.7k
views
Visualizing gene counts and variance stabilization
deseq2 rnaseq variancestabilizingtransformation visualization
updated 8.3 years ago by 40k • written 8.3 years ago by ▴ 40
0
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1
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2.4k
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Warning in lfproc when using rlog or varianceStabilisingTransformation from DESeq2
DESeq2 rlog varianceStabilizingTransformation lfproc
updated 8.4 years ago by 40k • written 8.4 years ago by • 0
22 results • Page 1 of 1
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.
Comment: collapseReplicates error after tximeta by Michael Love 40k
A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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