Showing : RUVSeq • reset
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 8 days ago by ★ 4.0k • written 11 weeks ago by • 0
0
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1
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199
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 7 weeks ago by 53k • written 8 weeks ago by • 0
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3
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358
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
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1
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1.2k
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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 7 months ago by 43k • written 8 months ago by • 0
2
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2
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877
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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
15 months ago BioinfGuru ▴ 70
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1.0k
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 16 months ago by 43k • written 16 months ago by • 0
1
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601
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
16 months ago Erdi ▴ 10
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532
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determine k during RUVSeq
RUVSeq RUVnormalize
18 months ago Ειρήνη • 0
2
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9
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1.8k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 months ago by 68k • written 19 months ago by • 0
3
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6
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1.6k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
19 months ago nhaus ▴ 70
3
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2
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1.0k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
21 months ago Shaimaa Gamal • 0
4
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3
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1.2k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
2
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3
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1.1k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
2
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5
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1.4k
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Batch-resolved visualization after RUVg normalization?
RUVSeq
22 months ago ctlong • 0
0
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6
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1.4k
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
5
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9
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2.8k
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Batch correction and repeated measures
RUVSeq sva limma
updated 19 months ago by 53k • written 2.2 years ago by ▴ 10
3
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5
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2.2k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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4
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1.4k
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.3 years ago anne.hoffrichter • 0
3
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12
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2.9k
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Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 10
1
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2
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1.5k
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.6 years ago AZ ▴ 30
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0
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751
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.7 years ago Luca • 0
1
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2
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1.8k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.7 years ago garbuzov • 0
3
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6
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1.9k
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RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.8 years ago • updated 2.7 years ago Zainab ▴ 20
0
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1
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1.2k
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RUV with K more than 1.
RUVSeq
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
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3
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1.5k
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question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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0
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811
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RUVg for SNAP-ChIP ?
RUVSeq
3.0 years ago Bogdan ▴ 670
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1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.4 years ago Tongjun • 0
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4
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3.7k
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Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.4 years ago Mohamed ▴ 30
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7
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2.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.4 years ago by 43k • written 3.5 years ago by ▴ 60
1
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1
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1.1k
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paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
2
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7
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2.4k
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CPM after RUVseq
RUVSeq CPM Normalization
3.5 years ago Jess • 0
0
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5
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6.0k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.9 years ago by ★ 5.0k • written 4.7 years ago by • 0
1
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1
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1.3k
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Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.1 years ago Mallory ▴ 10
1
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5
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2.6k
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how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 15 months ago by ▴ 70 • written 4.4 years ago by ▴ 60
2
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6
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6.1k
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Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago • updated 4.4 years ago reganhayward • 0
2
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2
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2.1k
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How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.6 years ago elizabethe819 • 0
0
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0
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988
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Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.7 years ago bioinfc • 0
0
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7
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2.5k
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RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.8 years ago by ▴ 980 • written 4.8 years ago by • 0
5
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6
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2.4k
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RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 20
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2
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2.0k
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
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7
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25k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
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0
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988
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"Frozen" RUVseq normalization
RUVseq machine learning
5.5 years ago acquaviva.massimo • 0
2
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6
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2.0k
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Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
2
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4
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3.0k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
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3
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1.5k
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unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
1
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4
replies
3.1k
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Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.0 years ago Arindam ▴ 80
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2
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2.3k
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Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.1 years ago by ▴ 980 • written 6.1 years ago by • 0
1
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1
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1.8k
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Using RUVs with known batches
ruvseq deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 30
0
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1
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1.0k
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[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
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0
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1.3k
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Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.5 years ago garbuzov • 0
108 results • Page 1 of 3
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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