Showing : ruvseq • reset
2
votes
2
replies
379
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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
5 weeks ago BioinfGuru ▴ 70
0
votes
1
reply
316
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 9 weeks ago by 42k • written 10 weeks ago by • 0
1
vote
0
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214
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
10 weeks ago Erdi ▴ 10
0
votes
0
replies
214
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determine k during RUVSeq
RUVSeq RUVnormalize
4 months ago Ειρήνη • 0
2
votes
9
replies
783
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 months ago by 67k • written 4 months ago by • 0
3
votes
6
replies
666
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 months ago nhaus ▴ 70
3
votes
2
replies
503
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
7 months ago Shaimaa Gamal • 0
4
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3
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598
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 7 months ago by 51k • written 7 months ago by • 0
2
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3
replies
576
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 7 months ago by 67k • written 7 months ago by • 0
2
votes
5
replies
694
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
8 months ago ctlong • 0
0
votes
6
replies
886
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 10 months ago by 42k • written 10 months ago by • 0
5
votes
9
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1.7k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 5 months ago by 51k • written 11 months ago by ▴ 10
3
votes
5
replies
1.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 12 months ago by ★ 4.4k • written 12 months ago by • 0
0
votes
4
replies
859
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
13 months ago anne.hoffrichter • 0
3
votes
12
replies
1.9k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 17 months ago by 42k • written 17 months ago by ▴ 10
1
vote
2
replies
1.1k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
17 months ago AZ ▴ 30
0
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0
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498
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
17 months ago Luca • 0
1
vote
2
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1.3k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
18 months ago garbuzov • 0
3
votes
6
replies
1.3k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
19 months ago • updated 18 months ago Zainab ▴ 10
0
votes
1
reply
841
views
RUV with K more than 1.
RUVSeq
updated 20 months ago by ★ 4.4k • written 20 months ago by ▴ 10
0
votes
3
replies
1.2k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 21 months ago by 42k • written 21 months ago by • 0
0
votes
0
replies
574
views
RUVg for SNAP-ChIP ?
RUVSeq
21 months ago Bogdan ▴ 670
0
votes
1
reply
766
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.2 years ago Tongjun • 0
0
votes
4
replies
2.6k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.2 years ago Mohamed ▴ 30
1
vote
7
replies
1.9k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.2 years ago by 42k • written 2.3 years ago by ▴ 50
1
vote
1
reply
864
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.3 years ago by 67k • written 2.3 years ago by ▴ 20
2
votes
7
replies
1.8k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.3 years ago Jess • 0
0
votes
5
replies
4.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.7 years ago by ★ 4.4k • written 3.5 years ago by • 0
1
vote
1
reply
919
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.9 years ago Mallory ▴ 10
1
vote
5
replies
1.9k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 6 weeks ago by ▴ 70 • written 3.2 years ago by ▴ 50
2
votes
6
replies
5.0k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.3 years ago • updated 3.2 years ago reganhayward • 0
2
votes
2
replies
1.5k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.4 years ago elizabethe819 • 0
0
votes
0
replies
730
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.5 years ago bioinfc • 0
0
votes
7
replies
1.8k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.6 years ago by ▴ 980 • written 3.6 years ago by • 0
5
votes
6
replies
1.8k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 20
0
votes
2
replies
1.5k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
0
votes
7
replies
22k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
0
votes
0
replies
726
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.3 years ago acquaviva.massimo • 0
2
votes
6
replies
1.5k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.3 years ago by 51k • written 4.3 years ago by • 0
2
votes
4
replies
2.1k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
0
votes
3
replies
1.1k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
1
vote
4
replies
2.5k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.8 years ago Arindam ▴ 80
0
votes
2
replies
1.8k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.9 years ago by ▴ 980 • written 4.9 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 30
0
votes
1
reply
817
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
0
replies
966
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.3 years ago garbuzov • 0
0
votes
2
replies
2.7k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.3 years ago by ▴ 980 • written 5.4 years ago by • 0
2
votes
4
replies
2.5k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.3 years ago by ▴ 980 • written 5.4 years ago by ▴ 250
0
votes
0
replies
909
views
RUVseq: Use of known controls with RUVg
RUVseq
5.4 years ago bio.erikson • 0
1
vote
3
replies
2.4k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.6 years ago by 51k • written 5.6 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: How to read OSCA book? by zr • 0
Got it, that had really confused me a bit, thank you for your help!
Comment: How to use removeBatchEffect for removing effect of multiple confounding variabl by James W. MacDonald 67k
Please don't add questions onto a four-year old post. Instead, start a new one. If you want to reference the old post, that's fine.
Answer: How to use removeBatchEffect for removing effect of multiple confounding variabl by bioinformata • 0
Is it feasible to remove batch effect with limma after variance stabilizing transformation of the gene expression , or is eough to use vst…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k
Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…
Votes
Answer: How to read OSCA book?
Answer: How to read OSCA book?
DESeq2 design and contrasts with 2 drug-treated and one control group
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
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