Showing : RUVseq • reset
7
votes
2
replies
3.2k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2 ruvseq spike-in time course time series
updated 6.4 years ago by ▴ 950 • written 6.4 years ago by ▴ 20
6
votes
7
replies
3.9k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
8.5 years ago tonja.r ▴ 80
5
votes
6
replies
1.6k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 20
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
5
votes
3
replies
2.5k
views
edgeR: annotation and isoform analysis alternatives
edgeR ruvseq rnaseq isoforms
9.0 years ago sergio.espeso-gil • 0
5
votes
4
replies
2.4k
views
Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
deseq2 ruvseq
updated 7.0 years ago by ▴ 950 • written 7.0 years ago by ▴ 10
4
votes
5
replies
2.6k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
4
votes
4
replies
2.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 660
4
votes
3
replies
380
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
8.8 years ago nickp60 • 0
3
votes
6
replies
305
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
3
votes
7
replies
2.1k
views
Batch effects between controls
batch-effect ruvseq
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 10
3
votes
9
replies
5.1k
views
DESeq2 results with RUVSeq values
deseq2 ruvseq sizefacotrs
updated 9.0 years ago by ▴ 950 • written 9.0 years ago by ★ 1.5k
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 13 months ago by 42k • written 13 months ago by ▴ 10
3
votes
6
replies
1.1k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
15 months ago • updated 14 months ago Zainab ▴ 10
3
votes
5
replies
891
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
3
votes
2
replies
317
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
3
votes
2
replies
2.6k
views
Normalisation before RUVg and RUV2?
ruvseq ruv
updated 9.0 years ago by ▴ 950 • written 9.0 years ago by ▴ 150
2
votes
2
replies
2.0k
views
RUVg with differential transcript expression?
ruvseq sleuth
updated 6.4 years ago by ▴ 950 • written 6.4 years ago by • 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()
3.0 years ago elizabethe819 • 0
2
votes
8
replies
2.5k
views
Issue with RUVs
ruvseq RUVs EDA
9.7 years ago • updated 9.6 years ago asif.zubair • 0
2
votes
12
replies
2.5k
views
LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
8.8 years ago Mark.Rogers • 0
2
votes
4
replies
1.7k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
2
votes
1
reply
1.5k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq RUV ruvnormalize ruvg
7.9 years ago anthonycolombo60 • 0
2
votes
6
replies
3.1k
views
RUVSeq DE analysis for data with replicate samples and 4 conditions
RUVSeq
updated 7.9 years ago by • 0 • written 8.7 years ago by ▴ 40
2
votes
5
replies
483
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago ctlong • 0
2
votes
2
replies
1.6k
views
Paired analysis and batch effects ?
ruvseq sva edger
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by ▴ 10
2
votes
6
replies
1.4k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
2
votes
6
replies
1.5k
views
effect of polyploidy level on RUVs normalisation
normalization ruvseq ruvnormalize ruvs eda
8.1 years ago thomas.wolfe • 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
2
votes
1
reply
1.3k
views
Decide normalisation method in RUVseq for RNAseq data
edger ruvseq rnaseq normalization ruvnormalize
updated 6.9 years ago by ▴ 950 • written 6.9 years ago by • 0
2
votes
4
replies
2.2k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.0 years ago by ▴ 950 • written 5.0 years ago by ▴ 250
2
votes
3
replies
2.1k
views
How to determine a set of empirical control 'genes' using RUVSeq
RUVSeq
updated 23 months ago by ▴ 30 • written 7.2 years ago by • 0
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
4
replies
1.8k
views
RUVseq design matrix for first pass of edger
ruvseq
written 8.4 years ago by ▴ 80
2
votes
7
replies
1.6k
views
CPM after RUVseq
RUVSeq CPM Normalization
24 months ago Jess • 0
2
votes
3
replies
1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
2
votes
9
replies
2.6k
views
Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 6.8 years ago by ▴ 950 • written 6.8 years ago by ▴ 80
1
vote
2
replies
872
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
13 months ago AZ ▴ 30
1
vote
2
replies
1.0k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
14 months ago garbuzov • 0
1
vote
2
replies
2.4k
views
RUVseq using RUVg most non-differential expressed genes
ruvseq
updated 8.5 years ago by ▴ 950 • written 8.5 years ago by ▴ 80
1
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4
replies
2.4k
views
RUVseq control genes - invalid subscript type 'list'
ruvseq
7.8 years ago eteleeb ▴ 10
1
vote
9
replies
2.7k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.6 years ago by ▴ 950 • written 5.6 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.9 years ago by ▴ 950 • written 5.9 years ago by • 0
1
vote
2
replies
1.0k
views
RUVSeq and Generalised Linear Mixed Model
ruvseq
updated 7.9 years ago by ▴ 950 • written 7.9 years ago by ▴ 10
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 6.5 years ago by ▴ 950 • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2 ruvseq covariates continuous vsd
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
1
vote
9
replies
2.6k
views
RUV: removing unwanted variation in RNA-seq
RUV ruvseq rnaseq
9.0 years ago sergio.espeso-gil • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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