Showing : ruvseq • reset
2
votes
2
replies
421
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
8 weeks ago BioinfGuru ▴ 70
0
votes
1
reply
376
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 3 months ago by 42k • written 3 months ago by • 0
1
vote
0
replies
237
views
RUVg spike-in assumption global expression
RUVSeq RUVnormalize
3 months ago Erdi ▴ 10
0
votes
0
replies
233
views
determine k during RUVSeq
RUVSeq RUVnormalize
4 months ago Ειρήνη • 0
2
votes
9
replies
841
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 5 months ago by 67k • written 5 months ago by • 0
3
votes
6
replies
725
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
6 months ago nhaus ▴ 70
3
votes
2
replies
522
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
8 months ago Shaimaa Gamal • 0
4
votes
3
replies
626
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
2
votes
3
replies
619
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 8 months ago by 67k • written 8 months ago by • 0
2
votes
5
replies
740
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
9 months ago ctlong • 0
0
votes
6
replies
915
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 10 months ago by 42k • written 11 months ago by • 0
5
votes
9
replies
1.8k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 5 months ago by 51k • written 12 months ago by ▴ 10
3
votes
5
replies
1.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 13 months ago by ★ 4.5k • written 13 months ago by • 0
0
votes
4
replies
891
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
14 months ago anne.hoffrichter • 0
3
votes
12
replies
1.9k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 17 months ago by 42k • written 18 months ago by ▴ 10
1
vote
2
replies
1.1k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
18 months ago AZ ▴ 30
0
votes
0
replies
515
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
18 months ago Luca • 0
1
vote
2
replies
1.3k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
18 months ago garbuzov • 0
3
votes
6
replies
1.3k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
20 months ago • updated 18 months ago Zainab ▴ 10
0
votes
1
reply
874
views
RUV with K more than 1.
RUVSeq
updated 21 months ago by ★ 4.5k • written 21 months ago by ▴ 10
0
votes
3
replies
1.2k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 22 months ago by 42k • written 22 months ago by • 0
0
votes
0
replies
601
views
RUVg for SNAP-ChIP ?
RUVSeq
22 months ago Bogdan ▴ 670
0
votes
1
reply
786
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.2 years ago Tongjun • 0
0
votes
4
replies
2.6k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.3 years ago Mohamed ▴ 30
1
vote
7
replies
1.9k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 50
1
vote
1
reply
884
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 20
2
votes
7
replies
1.9k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.4 years ago Jess • 0
0
votes
5
replies
4.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.7 years ago by ★ 4.5k • written 3.6 years ago by • 0
1
vote
1
reply
945
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.0 years ago • updated 2.9 years ago Mallory ▴ 10
1
vote
5
replies
1.9k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 9 weeks ago by ▴ 70 • written 3.3 years ago by ▴ 50
2
votes
6
replies
5.1k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.3 years ago reganhayward • 0
2
votes
2
replies
1.6k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.4 years ago elizabethe819 • 0
0
votes
0
replies
745
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.5 years ago bioinfc • 0
0
votes
7
replies
1.9k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.7 years ago by ▴ 980 • written 3.7 years ago by • 0
5
votes
6
replies
1.8k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 20
0
votes
2
replies
1.5k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
0
votes
7
replies
22k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
votes
0
replies
743
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.4 years ago acquaviva.massimo • 0
2
votes
6
replies
1.6k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.4 years ago by 51k • written 4.4 years ago by • 0
2
votes
4
replies
2.1k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
0
votes
3
replies
1.1k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
1
vote
4
replies
2.5k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.9 years ago Arindam ▴ 80
0
votes
2
replies
1.8k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.0 years ago by ▴ 980 • written 5.0 years ago by • 0
1
vote
1
reply
1.5k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 30
0
votes
1
reply
837
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
0
replies
986
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.3 years ago garbuzov • 0
0
votes
2
replies
2.7k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.3 years ago by ▴ 980 • written 5.5 years ago by • 0
2
votes
4
replies
2.5k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.4 years ago by ▴ 980 • written 5.4 years ago by ▴ 250
0
votes
0
replies
929
views
RUVseq: Use of known controls with RUVg
RUVseq
5.4 years ago bio.erikson • 0
1
vote
3
replies
2.5k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.6 years ago by 51k • written 5.7 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable by gabry.scata ▴ 10
Hi James, and thank you so much for your quick reply! That's great to know that I have installed successfully the packages i wanted. What …
Comment: pathview error "negative length vectors are not allowed by Evan • 0
Same for N-glycan metabolism-- fails with `same.layer = TRUE` , smudges and comet-like shading with `same.layer = FALSE`, crowded web with …
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Technically it's fitting an analysis of deviance (ANODEV) test, but the principle is the same - deviance, like the likelihood, measures goo…
Comment: How to conduct maSigPro analysis with only one condition? by James W. MacDonald 67k
Yeah, it's fine. What `maSigPro` does in this case is to reformulate the data. Your design has columns that are not useful, and `maSigPro` …
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable by James W. MacDonald 67k
You have installed the packages you wanted: ``` package BiocVersion successfully unpacked and MD5 sums checked package LEA success…
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Comment: How to conduct maSigPro analysis with only one condition?
Comment: How to conduct maSigPro analysis with only one condition?
Comment: Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentificat
Answer: How to conduct maSigPro analysis with only one condition?
Answer: How to conduct maSigPro analysis with only one condition?
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