Showing : ruvseq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 9 weeks ago by ★ 4.0k • written 4 months ago by • 0
0
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1
reply
255
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
0
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3
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414
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
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1
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1.3k
views
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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942
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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
17 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 18 months ago by 43k • written 18 months ago by • 0
1
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0
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647
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
18 months ago Erdi ▴ 10
0
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0
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594
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determine k during RUVSeq
RUVSeq RUVnormalize
20 months ago Ειρήνη • 0
2
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9
replies
1.9k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 months ago by 68k • written 21 months ago by • 0
3
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6
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1.8k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
21 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
23 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 23 months ago by 53k • written 23 months ago by • 0
2
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3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
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5
replies
1.6k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
2.0 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 2.2 years ago by • 0
5
votes
9
replies
3.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 21 months ago by 53k • written 2.3 years ago by ▴ 10
3
votes
5
replies
2.3k
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
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2
replies
1.6k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.8 years ago AZ ▴ 20
0
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0
replies
798
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.8 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
2.8 years ago garbuzov • 0
3
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6
replies
2.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
3.0 years ago • updated 2.8 years ago Zainab ▴ 20
0
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1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 10
0
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3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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0
replies
857
views
RUVg for SNAP-ChIP ?
RUVSeq
3.1 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
3.5 years ago Tongjun • 0
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4
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3.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
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 3.6 years ago by 43k • written 3.6 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
votes
7
replies
2.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.7 years ago Jess • 0
0
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5
replies
6.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.0 years ago by ★ 5.0k • written 4.8 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 • updated 4.2 years ago Mallory ▴ 10
1
vote
5
replies
2.7k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 17 months ago by ▴ 70 • written 4.6 years ago by ▴ 60
2
votes
6
replies
6.2k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.6 years ago reganhayward • 0
2
votes
2
replies
2.2k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.7 years ago elizabethe819 • 0
0
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0
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1.0k
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.8 years ago bioinfc • 0
0
votes
7
replies
2.6k
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 5.3 years ago by 68k • written 5.3 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
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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
replies
1.0k
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 5.7 years ago by 53k • written 5.7 years ago by • 0
2
votes
4
replies
3.2k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
3
replies
1.6k
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
2.4k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.3 years ago by ▴ 980 • written 6.3 years ago by • 0
1
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1
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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 6.6 years ago by 43k • written 6.6 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
6.6 years ago garbuzov • 0
108 results • Page 1 of 3
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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