Showing : ruvseq • reset
3
votes
5
replies
196
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 12 days ago by ★ 3.4k • written 12 days ago by • 0
0
votes
4
replies
262
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
7 weeks ago anne.hoffrichter • 0
3
votes
12
replies
779
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 5 months ago by 40k • written 5 months ago by ▴ 10
1
vote
2
replies
380
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
5 months ago AZ ▴ 30
0
votes
0
replies
170
views
Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
5 months ago Luca • 0
1
vote
2
replies
529
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
6 months ago garbuzov • 0
3
votes
6
replies
592
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
7 months ago • updated 6 months ago Zainab • 0
0
votes
1
reply
338
views
RUV with K more than 1.
RUVSeq
updated 8 months ago by ★ 3.4k • written 8 months ago by ▴ 10
0
votes
3
replies
537
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 9 months ago by 40k • written 9 months ago by • 0
0
votes
0
replies
272
views
RUVg for SNAP-ChIP ?
RUVSeq
9 months ago Bogdan ▴ 660
0
votes
1
reply
391
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
14 months ago Tongjun • 0
0
votes
4
replies
1.4k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
15 months ago Mohamed ▴ 20
1
vote
7
replies
1.1k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 15 months ago by 40k • written 15 months ago by ▴ 50
1
vote
1
reply
525
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 16 months ago by 63k • written 16 months ago by • 0
2
votes
7
replies
1.1k
views
CPM after RUVseq
RUVSeq CPM Normalization
16 months ago Jess • 0
0
votes
5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 20 months ago by ★ 3.4k • written 2.5 years ago by • 0
0
votes
1
reply
502
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
23 months ago Mallory • 0
1
vote
4
replies
1.1k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.3 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
3.8k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.3 years ago reganhayward • 0
2
votes
2
replies
1.0k
views
How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
2.4 years ago elizabethe819 • 0
0
votes
0
replies
469
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
2.5 years ago bioinfc • 0
0
votes
7
replies
1.1k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 2.6 years ago by ▴ 920 • written 2.6 years ago by • 0
5
votes
6
replies
1.3k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 20
0
votes
2
replies
1.1k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 3.3 years ago by 63k • written 3.3 years ago by • 0
0
votes
7
replies
19k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
0
votes
0
replies
424
views
"Frozen" RUVseq normalization
RUVseq machine learning
3.3 years ago acquaviva.massimo • 0
2
votes
6
replies
959
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 3.4 years ago by 48k • written 3.4 years ago by • 0
2
votes
4
replies
1.2k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
0
votes
3
replies
702
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
1
vote
4
replies
1.8k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
3.9 years ago ag1805x ▴ 80
0
votes
2
replies
1.2k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.0 years ago by ▴ 920 • written 4.0 years ago by • 0
1
vote
1
reply
1.0k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.1 years ago by 40k • written 4.1 years ago by ▴ 10
0
votes
1
reply
543
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.3 years ago by 40k • written 4.3 years ago by • 0
0
votes
0
replies
652
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
4.3 years ago garbuzov • 0
0
votes
2
replies
2.2k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 4.3 years ago by ▴ 920 • written 4.4 years ago by • 0
2
votes
4
replies
1.7k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 4.4 years ago by ▴ 920 • written 4.4 years ago by ▴ 250
0
votes
0
replies
599
views
RUVseq: Use of known controls with RUVg
RUVseq
4.4 years ago bio.erikson • 0
1
vote
3
replies
1.7k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 660
4
votes
4
replies
1.5k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 660
0
votes
1
reply
881
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 4.8 years ago by 40k • written 4.8 years ago by ▴ 50
0
votes
0
replies
982
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
4.8 years ago kbobowik • 0
0
votes
8
replies
1.7k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 4.9 years ago by ▴ 920 • written 4.9 years ago by • 0
0
votes
2
replies
1.6k
views
determine k during RUVSeq
ruvseq
updated 4.9 years ago by ▴ 920 • written 4.9 years ago by • 0
1
vote
9
replies
2.1k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 5.0 years ago by ▴ 920 • written 5.0 years ago by ▴ 10
2
votes
3
replies
1.0k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 5.1 years ago by 63k • written 5.1 years ago by • 0
1
vote
3
replies
1.2k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.2 years ago by ▴ 920 • written 5.2 years ago by • 0
2
votes
2
replies
1.7k
views
RUVg with differential transcript expression?
ruvseq sleuth
updated 5.7 years ago by ▴ 920 • written 5.7 years ago by • 0
6
votes
2
replies
2.7k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2 ruvseq spike-in time course time series
updated 5.8 years ago by ▴ 920 • written 5.8 years ago by ▴ 20
0
votes
3
replies
1.6k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 5.8 years ago by 40k • written 5.8 years ago by • 0
1
vote
1
reply
1.3k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 5.9 years ago by ▴ 920 • written 5.9 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DataFrame Construction With Non-standard Column by ATpoint ★ 3.4k
Out of interest, `SimpleList()` works without `I()`, why is that?
Answer: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
You need to protect the list by wrapping it in `I()`, otherwise the `DataFrame()` constructor interprets it as a list of 3 columns (so it t…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Votes
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Awards • All
Popular Question to Wolfgang Huber 13k
Popular Question to Martin Morgan 25k
Popular Question to Bogdan ▴ 660
Popular Question to Gordon Smyth 48k
Popular Question to Manmohit • 0
Locations • All
Ghent, Belgium, just now
India, 4 minutes ago
Sweden, 5 minutes ago
Italy, 7 minutes ago
Germany, 10 minutes ago
Traffic: 808 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