Showing : RUVSeq • reset
0
votes
1
reply
285
views
Questions about pseudo counts from RUVSeq
RUVSeq
updated 5 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
232
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 11 weeks ago by 53k • written 12 weeks ago by • 0
0
votes
3
replies
385
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
1
reply
1.2k
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
updated 8 months ago by 43k • written 9 months ago by • 0
2
votes
2
replies
900
views
Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
16 months ago BioinfGuru ▴ 70
0
votes
1
reply
1.0k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 17 months ago by 43k • written 17 months ago by • 0
1
vote
0
replies
630
views
RUVg spike-in assumption global expression
RUVSeq RUVnormalize
17 months ago Erdi ▴ 10
0
votes
0
replies
560
views
determine k during RUVSeq
RUVSeq RUVnormalize
19 months ago Ειρήνη • 0
2
votes
9
replies
1.9k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 20 months ago by 68k • written 20 months ago by • 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
20 months ago nhaus ▴ 70
3
votes
2
replies
1.1k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago • updated 22 months ago Shaimaa Gamal • 0
4
votes
3
replies
1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
votes
5
replies
1.5k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
23 months ago ctlong • 0
0
votes
6
replies
1.4k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 months ago by 53k • written 2.3 years ago by ▴ 10
3
votes
5
replies
2.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
4
replies
1.4k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.4 years ago anne.hoffrichter • 0
3
votes
12
replies
3.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.7 years ago AZ ▴ 30
0
votes
0
replies
774
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.7 years ago Luca • 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.8 years ago garbuzov • 0
3
votes
6
replies
1.9k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.9 years ago • updated 2.8 years ago Zainab ▴ 20
0
votes
1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
0
votes
3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
votes
0
replies
836
views
RUVg for SNAP-ChIP ?
RUVSeq
3.1 years ago Bogdan ▴ 670
0
votes
1
reply
1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.5 years ago Tongjun • 0
0
votes
4
replies
3.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.5 years ago Mohamed ▴ 30
1
vote
7
replies
2.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 3.5 years ago by 43k • written 3.6 years ago by ▴ 60
1
vote
1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 20
2
votes
7
replies
2.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.6 years ago Jess • 0
0
votes
5
replies
6.1k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.0 years ago by ★ 5.0k • written 4.8 years ago by • 0
1
vote
1
reply
1.3k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.2 years ago Mallory ▴ 10
1
vote
5
replies
2.7k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 17 months ago by ▴ 70 • written 4.5 years ago by ▴ 60
2
votes
6
replies
6.2k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago reganhayward • 0
2
votes
2
replies
2.1k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.7 years ago elizabethe819 • 0
0
votes
0
replies
1.0k
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.8 years ago bioinfc • 0
0
votes
7
replies
2.5k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.9 years ago by ▴ 980 • written 4.9 years ago by • 0
5
votes
6
replies
2.4k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 20
0
votes
2
replies
2.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
7
replies
25k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
0
replies
1.0k
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.6 years ago acquaviva.massimo • 0
2
votes
6
replies
2.1k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
2
votes
4
replies
3.1k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.6 years ago by 68k • written 5.7 years ago by • 0
0
votes
3
replies
1.6k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
1
vote
4
replies
3.1k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
6.1 years ago Arindam ▴ 80
0
votes
2
replies
2.4k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.2 years ago by ▴ 980 • written 6.2 years ago by • 0
1
vote
1
reply
1.9k
views
Using RUVs with known batches
ruvseq deseq2
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
0
replies
1.3k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.6 years ago garbuzov • 0
108 results • Page 1 of 3
Recent ...
Replies
Answer: blockwiseModule crashes in the end and doesn't generate modules by Daniel • 0
Queria compartir mi experiencia con [https://jugabet.cl/football/live/1][1] . Esta seccion ofrece cobertura en vivo de futbol, con marcado…
Comment: Empty boxes in treemap plot rrvgo package by TikTsokaasocissalpc • 0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis by adam80haynes • 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital by TikTsokaasocissalpc • 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes by TikTsokaasocissalpc • 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Votes
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Istvan Albert ▴ 50
Popular Question to Dario Strbenac ★ 1.6k
Locations • All
Ireland, 56 minutes ago
The city by the bay, 1 hour ago
United States, 1 hour ago
Ukraine, 2 hours ago
United States, 3 hours ago
Traffic: 1429 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