Showing : RUVseq • reset
0
votes
6
replies
326
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 14 days ago by 41k • written 5 weeks ago by • 0
5
votes
8
replies
635
views
Batch correction and repeated measures
RUVSeq sva limma
written 10 weeks ago by ▴ 10
3
votes
5
replies
389
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 12 weeks ago by ★ 3.6k • written 12 weeks ago by • 0
0
votes
4
replies
374
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
4 months ago anne.hoffrichter • 0
3
votes
12
replies
1.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 7 months ago by 41k • written 7 months ago by ▴ 10
1
vote
2
replies
528
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
7 months ago AZ ▴ 30
0
votes
0
replies
248
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
8 months ago Luca • 0
1
vote
2
replies
728
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
8 months ago garbuzov • 0
3
votes
6
replies
789
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
10 months ago • updated 8 months ago Zainab • 0
0
votes
1
reply
476
views
RUV with K more than 1.
RUVSeq
updated 10 months ago by ★ 3.6k • written 10 months ago by ▴ 10
0
votes
3
replies
717
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 11 months ago by 41k • written 12 months ago by • 0
0
votes
0
replies
347
views
RUVg for SNAP-ChIP ?
RUVSeq
12 months ago Bogdan ▴ 670
0
votes
1
reply
475
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
17 months ago Tongjun • 0
0
votes
4
replies
1.7k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
17 months ago Mohamed ▴ 20
1
vote
7
replies
1.3k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 17 months ago by 41k • written 18 months ago by ▴ 50
1
vote
1
reply
616
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 18 months ago by 64k • written 18 months ago by ▴ 20
2
votes
7
replies
1.3k
views
CPM after RUVseq
RUVSeq CPM Normalization
18 months ago Jess • 0
0
votes
5
replies
2.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 23 months ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
1
reply
583
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.2 years ago • updated 2.1 years ago Mallory • 0
1
vote
4
replies
1.3k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.5 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
4.0k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.5 years ago reganhayward • 0
2
votes
2
replies
1.1k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
2.6 years ago elizabethe819 • 0
0
votes
0
replies
529
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
2.7 years ago bioinfc • 0
0
votes
7
replies
1.3k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 2.8 years ago by ▴ 930 • written 2.8 years ago by • 0
5
votes
6
replies
1.4k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.2 years ago by 64k • written 3.2 years ago by ▴ 20
0
votes
2
replies
1.2k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 3.5 years ago by 64k • written 3.5 years ago by • 0
0
votes
7
replies
20k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
0
votes
0
replies
494
views
"Frozen" RUVseq normalization
RUVseq machine learning
3.5 years ago acquaviva.massimo • 0
2
votes
6
replies
1.1k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 3.6 years ago by 49k • written 3.6 years ago by • 0
2
votes
4
replies
1.3k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 3.6 years ago by 64k • written 3.6 years ago by • 0
0
votes
3
replies
785
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 3.8 years ago by 64k • written 3.8 years ago by • 0
1
vote
4
replies
1.9k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.1 years ago ag1805x ▴ 80
0
votes
2
replies
1.3k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.2 years ago by ▴ 930 • written 4.2 years ago by • 0
1
vote
1
reply
1.1k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ▴ 10
0
votes
1
reply
615
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
0
replies
728
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.5 years ago garbuzov • 0
0
votes
2
replies
2.3k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 4.5 years ago by ▴ 930 • written 4.6 years ago by • 0
2
votes
4
replies
1.8k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 4.6 years ago by ▴ 930 • written 4.6 years ago by ▴ 250
0
votes
0
replies
684
views
RUVseq: Use of known controls with RUVg
RUVseq
4.6 years ago bio.erikson • 0
1
vote
3
replies
1.9k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 4.8 years ago by 49k • written 4.8 years ago by ▴ 660
4
votes
4
replies
1.7k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 4.8 years ago by 49k • written 4.8 years ago by ▴ 660
0
votes
1
reply
956
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 50
0
votes
0
replies
1.1k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.0 years ago kbobowik • 0
0
votes
8
replies
1.9k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 5.1 years ago by ▴ 930 • written 5.1 years ago by ▴ 10
0
votes
2
replies
1.7k
views
determine k during RUVSeq
ruvseq
updated 5.1 years ago by ▴ 930 • written 5.1 years ago by ▴ 10
1
vote
9
replies
2.3k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.2 years ago by ▴ 930 • written 5.2 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 5.3 years ago by 64k • written 5.3 years ago by • 0
1
vote
3
replies
1.3k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.4 years ago by ▴ 930 • written 5.4 years ago by • 0
2
votes
2
replies
1.8k
views
RUVg with differential transcript expression?
ruvseq sleuth
updated 5.9 years ago by ▴ 930 • written 5.9 years ago by • 0
7
votes
2
replies
2.9k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2 ruvseq spike-in time course time series
updated 6.0 years ago by ▴ 930 • written 6.0 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Answer: WGCNA documentation not available by James W. MacDonald 64k
Although people sometimes ask questions about WGCNA on this support site, it's not a Bioconductor package and therefore off-topic. Peter La…
Comment: ATACseqQC shiftGAlignmentsList() problem by Ou, Jianhong ★ 1.3k
try: `gal1 <- shiftGAlignmentsList(gal, outbam='3-AL1_Tn5_shift.bam')`. I will try to figure out why the memory is so high.
Comment: ATACseqQC shiftGAlignmentsList() problem by jfmay • 0
Thanks for your response. The version of ATACseqQC I'm using is 1.26.0. I tried to set bigFile=TRUE. The resulting object *gal1* still ends…
Answer: biomaRt_getBM_Failed to collect lazy table by James W. MacDonald 64k
That's an old bug that you should be able to fix by updating. I can't remember what package, although `db_collect` comes from `dbplyr` (and…
Comment: rDGIdb package inconsistency with web interface by christopherjamessteel1990 • 0
I went on https://www.dgidb.org/api and searched "RPS3A" and got the below result. Not sure how you got something different. There is certa…
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Answer: ScRNAseq analysis scran :: quickcluster Error
Comment: Ensembl down???
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and
Comment: Ensembl down???
Answer: SingleR annotation of several slots/patients
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