Showing : ruvseq • reset
0
votes
0
replies
237
views
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
14 days ago Simran • 0
2
votes
2
replies
614
views
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
0
votes
1
reply
698
views
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
vote
0
replies
375
views
RUVg spike-in assumption global expression
RUVSeq RUVnormalize
9 months ago Erdi ▴ 10
0
votes
0
replies
363
views
determine k during RUVSeq
RUVSeq RUVnormalize
10 months ago Ειρήνη • 0
2
votes
9
replies
1.3k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 11 months ago by 68k • written 11 months ago by • 0
3
votes
6
replies
1.2k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
12 months ago nhaus ▴ 70
3
votes
2
replies
704
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
14 months ago Shaimaa Gamal • 0
4
votes
3
replies
886
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 14 months ago by 52k • written 14 months ago by • 0
2
votes
3
replies
825
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
5
replies
1.1k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
15 months ago ctlong • 0
0
votes
6
replies
1.1k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 16 months ago by 43k • written 17 months ago by • 0
5
votes
9
replies
2.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 11 months ago by 52k • written 18 months ago by ▴ 10
3
votes
5
replies
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
0
votes
4
replies
1.1k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
20 months ago anne.hoffrichter • 0
3
votes
12
replies
2.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 23 months ago by 43k • written 24 months ago by ▴ 10
1
vote
2
replies
1.3k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
24 months ago AZ ▴ 30
0
votes
0
replies
619
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.0 years ago Luca • 0
1
vote
2
replies
1.5k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.0 years ago garbuzov • 0
3
votes
6
replies
1.6k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.2 years ago • updated 2.0 years ago Zainab ▴ 20
0
votes
1
reply
1.1k
views
RUV with K more than 1.
RUVSeq
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by ▴ 10
0
votes
3
replies
1.3k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.3 years ago by 43k • written 2.4 years ago by • 0
0
votes
0
replies
698
views
RUVg for SNAP-ChIP ?
RUVSeq
2.3 years ago Bogdan ▴ 670
0
votes
1
reply
923
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.7 years ago Tongjun • 0
0
votes
4
replies
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
vote
7
replies
2.2k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 60
1
vote
1
reply
997
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
votes
7
replies
2.1k
views
CPM after RUVseq
RUVSeq CPM Normalization
2.9 years ago Jess • 0
0
votes
5
replies
5.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.2 years ago by ★ 4.8k • written 4.0 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 • updated 3.4 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
votes
6
replies
5.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.8 years ago reganhayward • 0
2
votes
2
replies
1.8k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.9 years ago elizabethe819 • 0
0
votes
0
replies
838
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.0 years ago bioinfc • 0
0
votes
7
replies
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
replies
2.1k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.5 years ago by 68k • written 4.6 years ago by ▴ 20
0
votes
2
replies
1.7k
views
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
votes
7
replies
24k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
0
replies
865
views
"Frozen" RUVseq normalization
RUVseq machine learning
4.9 years ago acquaviva.massimo • 0
2
votes
6
replies
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 4.9 years ago by 68k • written 4.9 years ago by • 0
0
votes
3
replies
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
0
votes
2
replies
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
vote
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
927
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
votes
0
replies
1.1k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.8 years ago garbuzov • 0
0
votes
2
replies
3.0k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.8 years ago by ▴ 980 • written 6.0 years ago by • 0
2
votes
4
replies
2.9k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.9 years ago by ▴ 980 • written 5.9 years ago by ▴ 260
0
votes
0
replies
1.0k
views
RUVseq: Use of known controls with RUVg
RUVseq
5.9 years ago bio.erikson • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Votes
Limma outputs different results for same sample?
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Awards • All
Popular Question to snijesh ▴ 200
Popular Question to Gordon Smyth 52k
Popular Question to pcantalupo ▴ 10
Popular Question to bioinformaticssrm2011 • 0
Popular Question to slizchap • 0
Locations • All
India, 2 minutes ago
Germany, 21 minutes ago
Sweden, 22 minutes ago
Sweden, 30 minutes ago
Switzerland, 33 minutes ago
Traffic: 984 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6