Showing : RUVSeq • reset
2
votes
2
replies
500
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
4 months ago BioinfGuru ▴ 70
0
votes
1
reply
499
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
0
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294
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
5 months ago Erdi ▴ 10
0
votes
0
replies
279
views
determine k during RUVSeq
RUVSeq RUVnormalize
7 months ago Ειρήνη • 0
2
votes
9
replies
1000
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 months ago by 67k • written 8 months ago by • 0
3
votes
6
replies
885
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
8 months ago nhaus ▴ 70
3
votes
2
replies
598
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 months ago Shaimaa Gamal • 0
4
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3
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738
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
2
votes
3
replies
690
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 months ago by 67k • written 10 months ago by • 0
2
votes
5
replies
831
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
11 months ago ctlong • 0
0
votes
6
replies
1000
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 13 months ago by 43k • written 13 months ago by • 0
5
votes
9
replies
2.0k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 8 months ago by 52k • written 15 months ago by ▴ 10
3
votes
5
replies
1.5k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
votes
4
replies
981
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
16 months ago anne.hoffrichter • 0
3
votes
12
replies
2.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
1
vote
2
replies
1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
20 months ago AZ ▴ 30
0
votes
0
replies
556
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
20 months ago Luca • 0
1
vote
2
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1.4k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
21 months ago garbuzov • 0
3
votes
6
replies
1.4k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
23 months ago • updated 21 months ago Zainab ▴ 20
0
votes
1
reply
943
views
RUV with K more than 1.
RUVSeq
updated 23 months ago by ★ 4.6k • written 23 months ago by ▴ 10
0
votes
3
replies
1.2k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
votes
0
replies
641
views
RUVg for SNAP-ChIP ?
RUVSeq
2.0 years ago Bogdan ▴ 670
0
votes
1
reply
846
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.4 years ago Tongjun • 0
0
votes
4
replies
2.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.5 years ago Mohamed ▴ 30
1
vote
7
replies
2.0k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 50
1
vote
1
reply
929
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 20
2
votes
7
replies
1.9k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.6 years ago Jess • 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.9 years ago by ★ 4.6k • written 3.7 years ago by • 0
1
vote
1
reply
998
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.2 years ago • updated 3.1 years ago Mallory ▴ 10
1
vote
5
replies
2.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 4 months ago by ▴ 70 • written 3.5 years ago by ▴ 50
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.5 years ago reganhayward • 0
2
votes
2
replies
1.7k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.6 years ago elizabethe819 • 0
0
votes
0
replies
787
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.7 years ago bioinfc • 0
0
votes
7
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2.0k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.9 years ago by ▴ 980 • written 3.9 years ago by • 0
5
votes
6
replies
1.9k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.2 years ago by 67k • written 4.3 years ago by ▴ 20
0
votes
2
replies
1.6k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
7
replies
23k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
0
replies
778
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.6 years ago acquaviva.massimo • 0
2
votes
6
replies
1.7k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
2
votes
4
replies
2.3k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
0
votes
3
replies
1.2k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
1
vote
4
replies
2.6k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.1 years ago Arindam ▴ 80
0
votes
2
replies
1.9k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.2 years ago by ▴ 980 • written 5.2 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 30
0
votes
1
reply
870
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
0
replies
1.0k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.5 years ago garbuzov • 0
0
votes
2
replies
2.8k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.5 years ago by ▴ 980 • written 5.7 years ago by • 0
2
votes
4
replies
2.6k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.6 years ago by ▴ 980 • written 5.6 years ago by ▴ 260
0
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0
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967
views
RUVseq: Use of known controls with RUVg
RUVseq
5.6 years ago bio.erikson • 0
1
vote
3
replies
2.6k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 660
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
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Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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