Showing : ruvseq • reset
2
votes
9
replies
392
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 12 days ago by • 0
3
votes
6
replies
279
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
26 days ago nhaus ▴ 30
3
votes
2
replies
298
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago • updated 12 weeks ago Shaimaa Gamal • 0
4
votes
3
replies
360
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
372
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
5
replies
467
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
3 months ago ctlong • 0
0
votes
6
replies
679
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 5 months ago by 42k • written 6 months ago by • 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 19 days ago by 50k • written 7 months ago by ▴ 10
3
votes
5
replies
861
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
4
replies
633
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 42k • written 12 months ago by ▴ 10
1
vote
2
replies
857
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
13 months ago • updated 12 months ago AZ ▴ 30
0
votes
0
replies
392
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
13 months ago Luca • 0
1
vote
2
replies
1.0k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
13 months ago garbuzov • 0
3
votes
6
replies
1.1k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
15 months ago • updated 13 months ago Zainab ▴ 10
0
votes
1
reply
653
views
RUV with K more than 1.
RUVSeq
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
0
votes
3
replies
990
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 16 months ago by 42k • written 17 months ago by • 0
0
votes
0
replies
465
views
RUVg for SNAP-ChIP ?
RUVSeq
17 months ago Bogdan ▴ 670
0
votes
1
reply
639
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
22 months ago Tongjun • 0
0
votes
4
replies
2.2k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
22 months ago Mohamed ▴ 30
1
vote
7
replies
1.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 22 months ago by 42k • written 23 months ago by ▴ 50
1
vote
1
reply
746
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 23 months ago by 65k • written 23 months ago by ▴ 20
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
23 months ago Jess • 0
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
1
vote
1
reply
773
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
votes
0
replies
645
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.1 years ago bioinfc • 0
0
votes
7
replies
1.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.2 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 3.6 years ago by 65k • written 3.6 years ago by ▴ 20
0
votes
2
replies
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 65k • written 3.9 years ago by • 0
0
votes
7
replies
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
votes
0
replies
596
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.0 years ago acquaviva.massimo • 0
2
votes
6
replies
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 65k • written 4.0 years ago by • 0
0
votes
3
replies
982
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.3 years ago by 65k • 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
1.5k
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
vote
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
724
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
844
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
0
votes
2
replies
2.5k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 4.9 years ago by ▴ 950 • written 5.1 years ago by • 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
votes
0
replies
818
views
RUVseq: Use of known controls with RUVg
RUVseq
5.0 years ago bio.erikson • 0
1
vote
3
replies
2.2k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 660
4
votes
4
replies
2.0k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.2 years ago by 50k • written 5.2 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
0
votes
8
replies
2.2k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 5.5 years ago by ▴ 950 • written 5.5 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
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Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
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Answer: How to save the DEXSeq results
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