Showing : RUVSeq • reset
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 1 day ago by 43k • written 29 days ago by • 0
2
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2
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639
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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
8 months ago BioinfGuru ▴ 70
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1
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728
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 9 months ago by 43k • written 9 months ago by • 0
1
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0
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392
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
9 months ago Erdi ▴ 10
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0
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382
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determine k during RUVSeq
RUVSeq RUVnormalize
11 months ago Ειρήνη • 0
2
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9
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1.4k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 months ago by 68k • written 12 months ago by • 0
3
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6
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1.2k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 months ago nhaus ▴ 70
3
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2
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723
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
14 months ago Shaimaa Gamal • 0
4
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3
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905
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 14 months ago by 52k • written 14 months ago by • 0
2
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3
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839
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 14 months ago by 68k • written 14 months ago by • 0
2
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5
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1.1k
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Batch-resolved visualization after RUVg normalization?
RUVSeq
15 months ago ctlong • 0
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6
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1.2k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 17 months ago by 43k • written 18 months ago by • 0
5
votes
9
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2.3k
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Batch correction and repeated measures
RUVSeq sva limma
updated 12 months ago by 52k • written 19 months ago by ▴ 10
3
votes
5
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1.8k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
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4
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1.1k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
21 months ago • updated 20 months ago anne.hoffrichter • 0
3
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12
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2.4k
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Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 10
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2
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1.3k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.0 years ago AZ ▴ 30
0
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0
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623
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.1 years ago Luca • 0
1
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2
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1.5k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.1 years ago garbuzov • 0
3
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6
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1.6k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.2 years ago • updated 2.1 years ago Zainab ▴ 20
0
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1
reply
1.1k
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RUV with K more than 1.
RUVSeq
updated 2.3 years ago by ★ 4.8k • written 2.3 years ago by ▴ 10
0
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3
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1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
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0
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705
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RUVg for SNAP-ChIP ?
RUVSeq
2.4 years ago Bogdan ▴ 670
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1
reply
935
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.8 years ago Tongjun • 0
0
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4
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3.2k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.8 years ago Mohamed ▴ 30
1
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7
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2.2k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.8 years ago by 43k • written 2.9 years ago by ▴ 60
1
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1
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1.0k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 20
2
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7
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2.1k
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CPM after RUVseq
RUVSeq CPM Normalization
2.9 years ago Jess • 0
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5
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5.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
1
vote
1
reply
1.1k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.5 years ago Mallory ▴ 10
1
vote
5
replies
2.3k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 8 months ago by ▴ 70 • written 3.8 years ago by ▴ 60
2
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6
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5.8k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.9 years ago • updated 3.8 years ago reganhayward • 0
2
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2
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1.9k
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How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.0 years ago elizabethe819 • 0
0
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0
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849
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Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.1 years ago bioinfc • 0
0
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7
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2.2k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.2 years ago by ▴ 980 • written 4.2 years ago by • 0
5
votes
6
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2.1k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 20
0
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2
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1.7k
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
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7
replies
24k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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869
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"Frozen" RUVseq normalization
RUVseq machine learning
4.9 years ago acquaviva.massimo • 0
2
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6
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1.8k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
2
votes
4
replies
2.6k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
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3
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1.3k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
vote
4
replies
2.8k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.4 years ago Arindam ▴ 80
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2
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2.1k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.5 years ago by ▴ 980 • written 5.5 years ago by • 0
1
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1
reply
1.6k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
0
votes
1
reply
938
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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0
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1.1k
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Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.9 years ago garbuzov • 0
0
votes
2
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3.0k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.9 years ago by ▴ 980 • written 6.0 years ago by • 0
2
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4
replies
2.9k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.9 years ago by ▴ 980 • written 6.0 years ago by ▴ 260
0
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0
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1.0k
views
RUVseq: Use of known controls with RUVg
RUVseq
6.0 years ago bio.erikson • 0
50 results • Page 1 of 1
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Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
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Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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