Showing : ruvseq • reset
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
8.8 years ago nickp60 • 0
3
votes
12
replies
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
2
votes
12
replies
2.5k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.8 years ago Mark.Rogers • 0
1
vote
9
replies
2.6k
views
RUV: removing unwanted variation in RNA-seq
RUV ruvseq rnaseq
9.0 years ago sergio.espeso-gil • 0
1
vote
9
replies
2.7k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.6 years ago by ▴ 950 • written 5.6 years ago by ▴ 10
3
votes
9
replies
5.1k
views
DESeq2 results with RUVSeq values
deseq2 ruvseq sizefacotrs
updated 9.0 years ago by ▴ 950 • written 9.0 years ago by ★ 1.5k
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
2
votes
9
replies
2.6k
views
Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 6.8 years ago by ▴ 950 • written 6.8 years ago by ▴ 80
2
votes
8
replies
2.5k
views
Issue with RUVs
ruvseq RUVs EDA
9.7 years ago • updated 9.6 years ago asif.zubair • 0
1
vote
8
replies
3.7k
views
Intepretation of RUVseq/edgeR logFC
RUVseq logFC edgeR
9.0 years ago Marie • 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
6
votes
7
replies
3.9k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
8.5 years ago tonja.r ▴ 80
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
24 months ago Jess • 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
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
3
votes
7
replies
2.1k
views
Batch effects between controls
batch-effect ruvseq
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 10
1
vote
7
replies
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
0
votes
6
replies
3.1k
views
How to use RUVseq with voom-limma for differential expression analysis?
ruvseq limma voom
updated 7.7 years ago by ▴ 950 • written 7.7 years ago by • 0
2
votes
6
replies
3.1k
views
RUVSeq DE analysis for data with replicate samples and 4 conditions
RUVSeq
updated 7.9 years ago by • 0 • written 8.7 years ago by ▴ 40
2
votes
6
replies
1.5k
views
effect of polyploidy level on RUVs normalisation
normalization ruvseq ruvnormalize ruvs eda
8.1 years ago thomas.wolfe • 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 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 65k • written 3.7 years ago by ▴ 20
3
votes
6
replies
305
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
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
0
votes
6
replies
696
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
3
votes
6
replies
1.1k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
15 months ago • updated 14 months ago Zainab ▴ 10
0
votes
5
replies
1.6k
views
Can Normalized cpm values be used as RUVs input
rnaseq ruvseq
updated 7.7 years ago by ▴ 950 • written 7.7 years ago by • 0
0
votes
5
replies
2.3k
views
RUVseq for microRNAs
ruvseq ruv microrna
8.8 years ago sergio.espeso-gil • 0
4
votes
5
replies
2.6k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
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 3.2 years ago by • 0
3
votes
5
replies
891
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
2
votes
5
replies
483
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago ctlong • 0
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.5 years ago j.viana • 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
1
vote
4
replies
2.4k
views
RUVseq control genes - invalid subscript type 'list'
ruvseq
7.8 years ago eteleeb ▴ 10
0
votes
4
replies
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
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
4
replies
649
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
2
votes
4
replies
1.8k
views
RUVseq design matrix for first pass of edger
ruvseq
written 8.4 years ago by ▴ 80
4
votes
4
replies
2.1k
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
5
votes
4
replies
2.4k
views
Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
deseq2 ruvseq
updated 7.0 years ago by ▴ 950 • written 7.0 years ago by ▴ 10
1
vote
4
replies
3.8k
views
Number of co-variables k in RUVSeq (RUVr)
rnaseq ruvseq RUVr edgeR
8.5 years ago • updated 8.4 years ago David R ▴ 90
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
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
2
votes
3
replies
1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
1
vote
3
replies
1.5k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.9 years ago by ▴ 950 • written 5.9 years ago by • 0
4
votes
3
replies
378
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
3
replies
1.9k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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