Showing : RUVseq • reset
0
votes
0
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122
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determine k during RUVSeq
RUVSeq RUVnormalize
6 weeks ago Ειρήνη • 0
2
votes
9
replies
553
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 weeks ago by 66k • written 9 weeks ago by • 0
3
votes
6
replies
448
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
11 weeks ago nhaus ▴ 50
3
votes
2
replies
380
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
4 months ago Shaimaa Gamal • 0
4
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3
replies
467
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 4 months ago by 51k • written 4 months ago by • 0
2
votes
3
replies
449
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 4 months ago by 66k • written 4 months ago by • 0
2
votes
5
replies
542
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
5 months ago ctlong • 0
0
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6
replies
757
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 7 months ago by 42k • written 8 months ago by • 0
5
votes
9
replies
1.5k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 10 weeks ago by 51k • written 9 months ago by ▴ 10
3
votes
5
replies
1.0k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 9 months ago by ★ 4.2k • written 9 months ago by • 0
0
votes
4
replies
710
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
11 months ago anne.hoffrichter • 0
3
votes
12
replies
1.7k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 14 months ago by 42k • written 14 months ago by ▴ 10
1
vote
2
replies
950
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
14 months ago AZ ▴ 30
0
votes
0
replies
424
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
15 months ago Luca • 0
1
vote
2
replies
1.1k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
15 months ago garbuzov • 0
3
votes
6
replies
1.2k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
17 months ago • updated 15 months ago Zainab ▴ 10
0
votes
1
reply
696
views
RUV with K more than 1.
RUVSeq
updated 17 months ago by ★ 4.2k • written 17 months ago by ▴ 10
0
votes
3
replies
1.0k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 18 months ago by 42k • written 19 months ago by • 0
0
votes
0
replies
493
views
RUVg for SNAP-ChIP ?
RUVSeq
19 months ago Bogdan ▴ 670
0
votes
1
reply
702
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
24 months ago • updated 23 months ago Tongjun • 0
0
votes
4
replies
2.3k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.0 years ago Mohamed ▴ 30
1
vote
7
replies
1.7k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.0 years ago by 42k • written 2.1 years ago by ▴ 50
1
vote
1
reply
776
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.1 years ago by 66k • written 2.1 years ago by ▴ 20
2
votes
7
replies
1.7k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.1 years ago Jess • 0
0
votes
5
replies
3.9k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.5 years ago by ★ 4.2k • written 3.3 years ago by • 0
1
vote
1
reply
817
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.7 years ago Mallory ▴ 10
1
vote
4
replies
1.7k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
3.0 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
4.8k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.1 years ago • updated 3.0 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()
3.2 years ago elizabethe819 • 0
0
votes
0
replies
672
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.3 years ago bioinfc • 0
0
votes
7
replies
1.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.4 years ago by ▴ 950 • written 3.4 years ago by • 0
5
votes
6
replies
1.7k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 20
0
votes
2
replies
1.4k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.0 years ago by 66k • written 4.0 years ago by • 0
0
votes
7
replies
21k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
0
votes
0
replies
648
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.1 years ago acquaviva.massimo • 0
2
votes
6
replies
1.5k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.1 years ago by 51k • written 4.1 years ago by • 0
2
votes
4
replies
1.8k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.2 years ago by 66k • written 4.2 years ago by • 0
0
votes
3
replies
1.0k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.4 years ago by 66k • written 4.4 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
4.6 years ago ag1805x ▴ 80
0
votes
2
replies
1.6k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.7 years ago by ▴ 950 • written 4.7 years ago by • 0
1
vote
1
reply
1.3k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.9 years ago by 42k • written 4.9 years ago by ▴ 30
0
votes
1
reply
754
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
votes
0
replies
882
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.1 years ago garbuzov • 0
0
votes
2
replies
2.6k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.1 years ago by ▴ 950 • written 5.2 years ago by • 0
2
votes
4
replies
2.3k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.1 years ago by ▴ 950 • written 5.1 years ago by ▴ 250
0
votes
0
replies
850
views
RUVseq: Use of known controls with RUVg
RUVseq
5.2 years ago bio.erikson • 0
1
vote
3
replies
2.3k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.4 years ago by 51k • written 5.4 years ago by ▴ 660
4
votes
4
replies
2.2k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.4 years ago by 51k • written 5.4 years ago by ▴ 660
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 50
0
votes
0
replies
1.3k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.6 years ago kbobowik • 0
50 results • Page 1 of 1
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Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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