Showing : RUVSeq • reset
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62
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determine k during RUVSeq
RUVSeq RUVnormalize
5 days ago Ειρήνη • 0
2
votes
9
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431
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 26 days ago by 66k • written 26 days ago by • 0
3
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6
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315
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
3
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2
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323
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
4
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3
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387
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
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3
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394
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
2
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5
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490
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Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago ctlong • 0
0
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6
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709
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 6 months ago by 42k • written 6 months ago by • 0
5
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9
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1.3k
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Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
3
votes
5
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902
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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4
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659
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
3
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12
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1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 13 months ago by 42k • written 13 months ago by ▴ 10
1
vote
2
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879
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
13 months ago AZ ▴ 30
0
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0
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401
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
13 months ago Luca • 0
1
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2
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1.0k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
14 months ago garbuzov • 0
3
votes
6
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1.1k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
15 months ago • updated 14 months ago Zainab ▴ 10
0
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1
reply
665
views
RUV with K more than 1.
RUVSeq
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
0
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0
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473
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RUVg for SNAP-ChIP ?
RUVSeq
17 months ago Bogdan ▴ 670
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3
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1.0k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
663
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
22 months ago Tongjun • 0
0
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4
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2.2k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
23 months ago Mohamed ▴ 30
1
vote
7
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1.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 23 months ago by 42k • written 23 months ago by ▴ 50
1
vote
1
reply
753
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 24 months ago by 66k • written 24 months ago by ▴ 20
2
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7
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1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.0 years ago • updated 24 months ago Jess • 0
1
vote
1
reply
783
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.6 years ago • updated 2.5 years ago Mallory ▴ 10
1
vote
4
replies
1.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.9 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
2
votes
2
replies
1.4k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.0 years ago elizabethe819 • 0
0
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0
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648
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Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.2 years ago bioinfc • 0
0
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5
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3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.4 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
votes
7
replies
1.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.3 years ago by ▴ 950 • written 3.3 years ago by • 0
5
votes
6
replies
1.6k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 20
0
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2
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1.3k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 3.9 years ago by 66k • written 3.9 years ago by • 0
0
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7
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21k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
0
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0
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615
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.0 years ago acquaviva.massimo • 0
2
votes
6
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1.4k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
2
votes
4
replies
1.7k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.0 years ago by 66k • written 4.0 years ago by • 0
0
votes
3
replies
990
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
1
vote
4
replies
2.3k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.5 years ago ag1805x ▴ 80
0
votes
2
replies
1.6k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.6 years ago by ▴ 950 • written 4.6 years ago by • 0
1
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1
reply
1.3k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 20
0
votes
1
reply
737
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.9 years ago by 42k • written 4.9 years ago by • 0
0
votes
0
replies
854
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.9 years ago garbuzov • 0
2
votes
4
replies
2.2k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.0 years ago by ▴ 950 • written 5.0 years ago by ▴ 250
0
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0
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831
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RUVseq: Use of known controls with RUVg
RUVseq
5.1 years ago bio.erikson • 0
0
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2
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2.5k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.0 years ago by ▴ 950 • written 5.1 years ago by • 0
4
votes
4
replies
2.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 660
1
vote
3
replies
2.2k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 660
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 50
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.5 years ago kbobowik • 0
50 results • Page 1 of 1
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Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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