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 3 days ago by 43k • written 4 weeks ago by • 0
2
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2
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642
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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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732
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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
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395
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
9 months ago Erdi ▴ 10
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383
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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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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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724
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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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907
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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
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3
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843
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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
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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
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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
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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
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5
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1.8k
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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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1.2k
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
21 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
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.0 years ago AZ ▴ 30
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624
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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
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RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.2 years ago • updated 2.1 years ago Zainab ▴ 20
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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
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3
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1.3k
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question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
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0
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707
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RUVg for SNAP-ChIP ?
RUVSeq
2.4 years ago Bogdan ▴ 670
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937
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.8 years ago Tongjun • 0
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4
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3.2k
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Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.8 years ago Mohamed ▴ 30
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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
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1
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1.0k
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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
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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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5.4k
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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
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1
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1.1k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.5 years ago Mallory ▴ 10
1
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5
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2.3k
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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
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6
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5.8k
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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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852
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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
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7
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2.2k
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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
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6
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2.1k
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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
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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
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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
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0
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873
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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
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Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
2
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4
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2.6k
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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
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3
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1.3k
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unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
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4
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2.8k
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Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.4 years ago Arindam ▴ 80
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2.1k
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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
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1.6k
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Using RUVs with known batches
ruvseq deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
0
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1
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940
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[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.9 years ago by 43k • written 5.9 years ago by • 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
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2
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3.0k
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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
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3.0k
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Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 6.0 years ago by ▴ 980 • written 6.0 years ago by ▴ 260
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0
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1.0k
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RUVseq: Use of known controls with RUVg
RUVseq
6.0 years ago bio.erikson • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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