Showing : RUVseq • reset
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45
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determine k during RUVSeq
RUVSeq RUVnormalize
1 day ago Ειρήνη • 0
2
votes
9
replies
426
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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
3
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6
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305
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
3
votes
2
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318
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
4
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3
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380
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
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3
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386
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
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5
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483
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Batch-resolved visualization after RUVg normalization?
RUVSeq
4 months ago ctlong • 0
0
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6
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697
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 5 months ago by 42k • written 6 months ago by • 0
5
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9
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1.3k
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Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
3
votes
5
replies
891
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
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4
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650
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
9 months ago anne.hoffrichter • 0
3
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12
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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
1
vote
2
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873
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
13 months ago AZ ▴ 30
0
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0
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400
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
13 months ago Luca • 0
1
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2
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1.0k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
14 months ago garbuzov • 0
3
votes
6
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1.1k
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RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
15 months ago • updated 14 months ago Zainab ▴ 10
0
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1
reply
661
views
RUV with K more than 1.
RUVSeq
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
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0
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470
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RUVg for SNAP-ChIP ?
RUVSeq
17 months ago Bogdan ▴ 670
0
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3
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1000
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question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
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1
reply
657
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
22 months ago Tongjun • 0
0
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4
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2.2k
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Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
23 months ago Mohamed ▴ 30
1
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7
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1.6k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 23 months ago by 42k • written 23 months ago by ▴ 50
1
vote
1
reply
752
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 24 months ago by 65k • written 24 months ago by ▴ 20
2
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7
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1.6k
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CPM after RUVseq
RUVSeq CPM Normalization
24 months ago Jess • 0
1
vote
1
reply
779
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
2.6 years ago • updated 2.5 years ago Mallory ▴ 10
1
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4
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1.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
2.9 years ago xiaofeiwang18266 ▴ 50
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 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
0
votes
0
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646
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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
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5
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3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
votes
7
replies
1.6k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 3.3 years ago by ▴ 950 • written 3.3 years ago by • 0
5
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6
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1.6k
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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
0
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2
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1.3k
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
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7
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21k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
0
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0
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609
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"Frozen" RUVseq normalization
RUVseq machine learning
4.0 years ago acquaviva.massimo • 0
2
votes
6
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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
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
0
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3
replies
988
views
unable to find inherited method inRUVG
ruvseq RUVSeq
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
1
vote
4
replies
2.3k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
4.5 years ago ag1805x ▴ 80
0
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2
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1.6k
views
Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 4.6 years ago by ▴ 950 • written 4.6 years ago by • 0
1
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1
reply
1.3k
views
Using RUVs with known batches
ruvseq deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 20
0
votes
1
reply
733
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 4.9 years ago by 42k • written 4.9 years ago by • 0
0
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0
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850
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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
2.2k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 5.0 years ago by ▴ 950 • written 5.0 years ago by ▴ 250
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0
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827
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RUVseq: Use of known controls with RUVg
RUVseq
5.0 years ago bio.erikson • 0
0
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2
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2.5k
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Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.0 years ago by ▴ 950 • written 5.1 years ago by • 0
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
1
vote
3
replies
2.2k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 5.2 years ago by 50k • written 5.3 years ago by ▴ 660
0
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1
reply
1.1k
views
merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 50
0
votes
0
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1.2k
views
Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
5.5 years ago kbobowik • 0
50 results • Page 1 of 1
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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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