Showing : RUVseq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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1
reply
283
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
0
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3
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451
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
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1
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1.3k
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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 9 months ago by 43k • written 10 months ago by • 0
2
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2
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964
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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
18 months ago BioinfGuru ▴ 70
0
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1
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1.1k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 19 months ago by 43k • written 19 months ago by • 0
1
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0
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665
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
19 months ago Erdi ▴ 10
0
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0
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627
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determine k during RUVSeq
RUVSeq RUVnormalize
21 months ago Ειρήνη • 0
2
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9
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2.0k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 months ago by 68k • written 22 months ago by • 0
3
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6
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1.9k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
22 months ago nhaus ▴ 70
3
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2
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1.2k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
2.0 years ago Shaimaa Gamal • 0
4
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3
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1.3k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
2
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5
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1.6k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
2.1 years ago ctlong • 0
0
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6
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1.5k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
5
votes
9
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3.0k
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Batch correction and repeated measures
RUVSeq sva limma
updated 22 months ago by 53k • written 2.4 years ago by ▴ 10
3
votes
5
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2.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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4
replies
1.5k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.5 years ago anne.hoffrichter • 0
3
votes
12
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3.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.8 years ago AZ ▴ 20
0
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0
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813
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.9 years ago Luca • 0
1
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2
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1.9k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.9 years ago garbuzov • 0
3
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6
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2.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
3.0 years ago • updated 2.9 years ago Zainab ▴ 20
0
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1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 10
0
votes
3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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0
replies
862
views
RUVg for SNAP-ChIP ?
RUVSeq
3.2 years ago Bogdan ▴ 670
0
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1
reply
1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.6 years ago Tongjun • 0
0
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4
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3.9k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.7 years ago • updated 3.6 years ago Mohamed ▴ 30
1
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7
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2.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 60
1
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1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.7 years ago by 68k • written 3.7 years ago by ▴ 20
2
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7
replies
2.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.7 years ago Jess • 0
0
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5
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6.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.1 years ago by ★ 5.0k • written 4.9 years ago by • 0
1
vote
1
reply
1.4k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.3 years ago Mallory ▴ 10
1
vote
5
replies
2.8k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 18 months ago by ▴ 70 • written 4.7 years ago by ▴ 60
2
votes
6
replies
6.3k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.7 years ago reganhayward • 0
2
votes
2
replies
2.3k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.8 years ago elizabethe819 • 0
0
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0
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1.1k
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.9 years ago bioinfc • 0
0
votes
7
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2.7k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 5.0 years ago by ▴ 980 • written 5.0 years ago by • 0
5
votes
6
replies
2.5k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 20
0
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2
replies
2.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
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0
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1.1k
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.7 years ago acquaviva.massimo • 0
2
votes
6
replies
2.1k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
2
votes
4
replies
3.4k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
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3
replies
1.7k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
1
vote
4
replies
3.2k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.2 years ago Arindam ▴ 80
0
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2
replies
2.5k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.4 years ago by ▴ 980 • written 6.4 years ago by • 0
1
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1
reply
1.9k
views
Using RUVs with known batches
ruvseq deseq2
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
0
votes
1
reply
1.1k
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
1.4k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.7 years ago garbuzov • 0
108 results • Page 1 of 3
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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