Showing : RUVseq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 17 days ago by ★ 4.0k • written 12 weeks ago by • 0
0
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1
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203
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 8 weeks ago by 53k • written 9 weeks ago by • 0
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3
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365
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
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1
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1.2k
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 7 months ago by 43k • written 8 months ago by • 0
2
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2
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884
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
16 months ago BioinfGuru ▴ 70
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1
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1.0k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 17 months ago by 43k • written 17 months ago by • 0
1
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608
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
17 months ago Erdi ▴ 10
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539
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determine k during RUVSeq
RUVSeq RUVnormalize
18 months ago Ειρήνη • 0
2
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9
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1.8k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 months ago by 68k • written 19 months ago by • 0
3
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6
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1.6k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
20 months ago nhaus ▴ 70
3
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2
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1.1k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
22 months ago Shaimaa Gamal • 0
4
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3
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1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
2
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3
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1.1k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
2
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5
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1.5k
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Batch-resolved visualization after RUVg normalization?
RUVSeq
23 months ago ctlong • 0
0
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6
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1.4k
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
5
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9
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2.8k
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Batch correction and repeated measures
RUVSeq sva limma
updated 19 months ago by 53k • written 2.2 years ago by ▴ 10
3
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5
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2.2k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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4
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1.4k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.3 years ago anne.hoffrichter • 0
3
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12
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2.9k
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Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
1
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2
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1.5k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.7 years ago • updated 2.6 years ago AZ ▴ 30
0
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0
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753
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.7 years ago Luca • 0
1
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2
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1.8k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.7 years ago garbuzov • 0
3
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6
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1.9k
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RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.9 years ago • updated 2.7 years ago Zainab ▴ 20
0
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1
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1.2k
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RUV with K more than 1.
RUVSeq
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
0
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3
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1.5k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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0
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822
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RUVg for SNAP-ChIP ?
RUVSeq
3.0 years ago Bogdan ▴ 670
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1
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1.1k
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.4 years ago Tongjun • 0
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4
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3.7k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.5 years ago • updated 3.4 years ago Mohamed ▴ 30
1
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7
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2.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 60
1
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1
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1.1k
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paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
2
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7
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2.4k
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CPM after RUVseq
RUVSeq CPM Normalization
3.5 years ago Jess • 0
0
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5
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6.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.9 years ago by ★ 5.0k • written 4.7 years ago by • 0
1
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1
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1.3k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.2 years ago • updated 4.1 years ago Mallory ▴ 10
1
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5
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2.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 16 months ago by ▴ 70 • written 4.5 years ago by ▴ 60
2
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6
replies
6.1k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago reganhayward • 0
2
votes
2
replies
2.1k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.6 years ago elizabethe819 • 0
0
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0
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995
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.7 years ago bioinfc • 0
0
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7
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2.5k
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RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.8 years ago by ▴ 980 • written 4.8 years ago by • 0
5
votes
6
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2.4k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 20
0
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2
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2.0k
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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0
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992
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.5 years ago acquaviva.massimo • 0
2
votes
6
replies
2.0k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
2
votes
4
replies
3.0k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
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3
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1.5k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
1
vote
4
replies
3.1k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.1 years ago Arindam ▴ 80
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2
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2.3k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.2 years ago by ▴ 980 • written 6.2 years ago by • 0
1
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1
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1.8k
views
Using RUVs with known batches
ruvseq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
0
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1
reply
1.1k
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
1.3k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.5 years ago garbuzov • 0
108 results • Page 1 of 3
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
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