Showing : ruvseq • reset
2
votes
4
replies
2.5k
views
RUVseq design matrix for first pass of edger
ruvseq
written 10.2 years ago by ▴ 80
0
votes
3
replies
2.5k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
0
votes
2
replies
2.5k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 6.4 years ago by ▴ 980 • written 6.4 years ago by • 0
1
vote
2
replies
2.4k
views
RUVSEq and VSD integration
deseq2 ruvseq covariates continuous vsd
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 10
3
votes
5
replies
2.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
1
reply
2.3k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq RUV ruvnormalize ruvg
9.6 years ago anthonycolombo60 • 0
2
votes
2
replies
2.3k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.8 years ago elizabethe819 • 0
2
votes
6
replies
2.2k
views
effect of polyploidy level on RUVs normalisation
normalization ruvseq ruvnormalize ruvs eda
9.8 years ago thomas.wolfe • 0
1
vote
1
reply
2.2k
views
RUVSeq installation problems
RUVSeq bioconductor biocinstaller
updated 10.1 years ago by ▴ 980 • written 10.1 years ago by • 0
0
votes
5
replies
2.2k
views
Can Normalized cpm values be used as RUVs input
rnaseq ruvseq
updated 9.5 years ago by ▴ 980 • written 9.5 years ago by • 0
2
votes
3
replies
2.2k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 7.6 years ago by ▴ 980 • written 7.6 years ago by • 0
1
vote
3
replies
2.2k
views
RUVseq coefficients for unwanted variance in design matrix
ruvseq edger deseq2
10.2 years ago tonja.r ▴ 80
2
votes
6
replies
2.2k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
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 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
1
reply
2.1k
views
How to generate heatmap for three groups
rnaseq ruvseq heatmap
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
1
vote
1
reply
2.1k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by ▴ 10
2
votes
9
replies
2.1k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 months ago by 68k • written 22 months ago by • 0
3
votes
6
replies
2.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
3.1 years ago • updated 2.9 years ago Zainab ▴ 20
2
votes
2
replies
2.0k
views
Paired analysis and batch effects ?
ruvseq sva edger
updated 10.0 years ago by ★ 7.9k • written 10.0 years ago by ▴ 10
1
vote
2
replies
1.9k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.9 years ago garbuzov • 0
1
vote
1
reply
1.9k
views
Using RUVs with known batches
ruvseq deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
3
votes
6
replies
1.9k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
22 months ago nhaus ▴ 70
0
votes
0
replies
1.8k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
7.3 years ago kbobowik • 0
2
votes
1
reply
1.8k
views
Decide normalisation method in RUVseq for RNAseq data
edger ruvseq rnaseq normalization ruvnormalize
updated 8.7 years ago by ▴ 980 • written 8.7 years ago by • 0
1
vote
2
replies
1.7k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.9 years ago AZ ▴ 20
0
votes
3
replies
1.7k
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
2
votes
5
replies
1.7k
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
2.1 years ago ctlong • 0
0
votes
1
reply
1.7k
views
RUVSeq installation problem
RUVSeq
11.5 years ago • updated 11.4 years ago davide risso ▴ 980
0
votes
3
replies
1.6k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
vote
1
reply
1.6k
views
Raw read count Vs EdgeR normzlized read count for RUVg normalization
rnaseq ruvseq normalization
updated 9.3 years ago by ▴ 980 • written 9.3 years ago by ▴ 40
0
votes
1
reply
1.6k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 50
0
votes
1
reply
1.6k
views
Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
dexseq ruvseq rnaseq
updated 9.1 years ago by ▴ 980 • written 9.1 years ago by ▴ 110
0
votes
6
replies
1.6k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
4
replies
1.5k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.6 years ago anne.hoffrichter • 0
1
vote
2
replies
1.5k
views
RUVSeq and Generalised Linear Mixed Model
ruvseq
updated 9.7 years ago by ▴ 980 • written 9.7 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
4.4 years ago • updated 4.3 years ago Mallory ▴ 10
0
votes
0
replies
1.4k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.7 years ago garbuzov • 0
0
votes
1
reply
1.3k
views
RUV with K more than 1.
RUVSeq
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 10
0
votes
1
reply
1.3k
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 10 months ago by 43k • written 11 months ago by • 0
4
votes
3
replies
1.3k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
votes
0
replies
1.3k
views
RUVseq: Use of known controls with RUVg
RUVseq
6.8 years ago bio.erikson • 0
0
votes
1
reply
1.3k
views
RNAseq Analysis using RUVs
rnaseq ruvseq r
updated 8.7 years ago by ▴ 980 • written 8.7 years ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 20
3
votes
2
replies
1.2k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
2.1 years ago Shaimaa Gamal • 0
0
votes
1
reply
1.2k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.6 years ago Tongjun • 0
0
votes
1
reply
1.2k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
1.1k
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
1.1k
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.9 years ago bioinfc • 0
0
votes
0
replies
1.1k
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.8 years ago acquaviva.massimo • 0
108 results • Page 2 of 3
Recent ...
Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Awards • All
Popular Question to Jaqueline • 0
Scholar to Gordon Smyth 53k
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Popular Question to Michael Love 43k
Locations • All
The city by the bay, 1 minute ago
Germany, 14 minutes ago
United States, 52 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1197 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