Showing : RUVseq • reset
3
votes
6
replies
206
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
7 days ago nhaus ▴ 30
3
votes
2
replies
258
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
4
votes
3
replies
314
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
3
replies
332
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
5
replies
425
views
Batch-resolved visualization after RUVg normalization?
RUVSeq
3 months ago ctlong • 0
0
votes
6
replies
653
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 4 months ago by 41k • written 5 months ago by • 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 1 day ago by 50k • written 6 months ago by ▴ 10
3
votes
5
replies
796
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
4
replies
607
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
8 months ago anne.hoffrichter • 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
1
vote
2
replies
818
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
12 months ago AZ ▴ 30
0
votes
0
replies
373
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
12 months ago Luca • 0
1
vote
2
replies
980
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
13 months ago garbuzov • 0
3
votes
6
replies
1.0k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
14 months ago • updated 13 months ago Zainab • 0
0
votes
1
reply
629
views
RUV with K more than 1.
RUVSeq
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 10
0
votes
0
replies
451
views
RUVg for SNAP-ChIP ?
RUVSeq
16 months ago Bogdan ▴ 670
0
votes
3
replies
966
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 16 months ago by 41k • written 16 months ago by • 0
0
votes
1
reply
607
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
21 months ago Tongjun • 0
0
votes
4
replies
2.1k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
22 months ago Mohamed ▴ 30
1
vote
7
replies
1.5k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 22 months ago by 41k • written 22 months ago by ▴ 50
1
vote
1
reply
732
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 23 months ago by 65k • written 23 months ago by ▴ 20
2
votes
7
replies
1.5k
views
CPM after RUVseq
RUVSeq CPM Normalization
23 months ago Jess • 0
1
vote
1
reply
744
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.5 years ago Mallory ▴ 10
1
vote
4
replies
1.5k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.8 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.8 years ago reganhayward • 0
2
votes
2
replies
1.3k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
3.0 years ago elizabethe819 • 0
0
votes
0
replies
627
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
3.1 years ago bioinfc • 0
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
7
replies
1.5k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.2 years ago by ▴ 950 • written 3.2 years ago by • 0
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 3.6 years ago by 65k • written 3.6 years ago by ▴ 20
0
votes
2
replies
1.3k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 3.8 years ago by 65k • written 3.8 years ago by • 0
0
votes
7
replies
21k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
0
votes
0
replies
574
views
"Frozen" RUVseq normalization
RUVseq machine learning
3.9 years ago acquaviva.massimo • 0
2
votes
6
replies
1.3k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
2
votes
4
replies
1.6k
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
0
votes
3
replies
957
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
1
vote
4
replies
2.2k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.4 years ago ag1805x ▴ 80
0
votes
2
replies
1.5k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.5 years ago by ▴ 950 • written 4.5 years ago by • 0
1
vote
1
reply
1.3k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 20
0
votes
1
reply
709
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
votes
0
replies
828
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.9 years ago garbuzov • 0
2
votes
4
replies
2.1k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 4.9 years ago by ▴ 950 • written 4.9 years ago by ▴ 250
0
votes
0
replies
798
views
RUVseq: Use of known controls with RUVg
RUVseq
5.0 years ago bio.erikson • 0
0
votes
2
replies
2.5k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 4.9 years ago by ▴ 950 • written 5.0 years ago by • 0
4
votes
4
replies
2.0k
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
1
vote
3
replies
2.1k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 660
0
votes
1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 50
0
votes
0
replies
1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.4 years ago kbobowik • 0
0
votes
8
replies
2.2k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 5.4 years ago by ▴ 950 • written 5.5 years ago by ▴ 10
0
votes
2
replies
2.0k
views
determine k during RUVSeq
ruvseq
updated 5.5 years ago by ▴ 950 • written 5.5 years ago by ▴ 10
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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