Showing : RUVSeq • reset
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determine k during RUVSeq
RUVSeq RUVnormalize
4 days ago Ειρήνη • 0
2
votes
9
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430
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 66k • written 25 days ago by • 0
5
votes
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
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6
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312
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
4
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16
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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
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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392
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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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488
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Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago ctlong • 0
2
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4
replies
1.8k
views
RUVseq design matrix for first pass of edger
ruvseq
written 8.4 years ago by ▴ 80
0
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6
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707
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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
3
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5
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900
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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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656
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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 13 months ago by 42k • written 13 months ago by ▴ 10
1
vote
2
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877
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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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400
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
13 months ago Luca • 0
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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
votes
1
reply
664
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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3
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1.0k
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question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
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0
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471
views
RUVg for SNAP-ChIP ?
RUVSeq
17 months ago Bogdan ▴ 670
0
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1
reply
661
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
2
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3
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2.1k
views
How to determine a set of empirical control 'genes' using RUVSeq
RUVSeq
updated 23 months ago by ▴ 30 • written 7.2 years ago by • 0
1
vote
7
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1.6k
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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
752
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
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.0 years ago • updated 24 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 2.4 years ago by ★ 4.1k • written 3.2 years ago by • 0
1
vote
1
reply
781
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
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1.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.9 years ago xiaofeiwang18266 ▴ 50
2
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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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647
views
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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7
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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
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 66k • 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
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0
replies
612
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 66k • written 4.0 years ago by • 0
0
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3
replies
989
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
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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
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
735
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
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0
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852
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 5.0 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
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0
replies
829
views
RUVseq: Use of known controls with RUVg
RUVseq
5.1 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 5.3 years ago by 50k • written 5.3 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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