Showing : ruvseq • reset
2
votes
9
replies
354
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 8 days ago by • 0
3
votes
6
replies
268
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
22 days ago nhaus ▴ 30
3
votes
2
replies
293
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
4
votes
3
replies
351
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
2
votes
3
replies
365
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
5
replies
458
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
3 months ago ctlong • 0
0
votes
6
replies
672
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 5 months ago by 41k • written 6 months ago by • 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 16 days ago by 50k • written 7 months ago by ▴ 10
3
votes
5
replies
849
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
627
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 41k • written 12 months ago by ▴ 10
1
vote
2
replies
852
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
12 months ago AZ ▴ 30
0
votes
0
replies
389
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 • 0
0
votes
1
reply
650
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
985
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 16 months ago by 41k • written 17 months ago by • 0
0
votes
0
replies
458
views
RUVg for SNAP-ChIP ?
RUVSeq
17 months ago Bogdan ▴ 670
0
votes
1
reply
630
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
22 months ago • updated 21 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 41k • written 23 months ago by ▴ 50
1
vote
1
reply
743
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
771
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
4.5k
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
640
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
1.5k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.2 years ago by ▴ 950 • written 3.2 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 41k • written 3.9 years ago by • 0
0
votes
0
replies
590
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
973
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
1
vote
4
replies
2.2k
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 4.7 years ago by 41k • written 4.7 years ago by ▴ 20
0
votes
1
reply
719
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
0
votes
0
replies
840
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 5.0 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
814
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 41k • 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
5.4 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
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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