Showing : RUVSeq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 3 months ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
290
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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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462
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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 10 months ago by 43k • written 11 months ago by • 0
2
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2
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968
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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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671
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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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634
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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
views
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
views
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
votes
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 2.1 years ago by • 0
2
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3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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5
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1.7k
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 2.3 years ago by 43k • written 2.3 years ago by • 0
5
votes
9
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3.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 22 months ago by 53k • written 2.4 years ago by ▴ 10
3
votes
5
replies
2.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.5 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
2.6 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 2.9 years ago by ▴ 10
1
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2
replies
1.7k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.9 years ago AZ ▴ 20
0
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0
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814
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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
votes
6
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2.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
3.1 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
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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
votes
0
replies
864
views
RUVg for SNAP-ChIP ?
RUVSeq
3.2 years ago Bogdan ▴ 670
0
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1
reply
1.2k
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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4.0k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.7 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
vote
1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 20
2
votes
7
replies
2.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.8 years ago Jess • 0
0
votes
5
replies
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
4.4 years ago • updated 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
replies
2.7k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 5.0 years ago by ▴ 980 • written 5.1 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 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
0
replies
1.1k
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.8 years ago acquaviva.massimo • 0
2
votes
6
replies
2.2k
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
votes
3
replies
1.7k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 6.1 years ago by 68k • written 6.1 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
6.3 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 6.6 years ago by 43k • written 6.6 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: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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