Showing : RUVseq • reset
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 20 days ago by 43k • written 6 weeks ago by • 0
2
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2
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658
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
9 months ago BioinfGuru ▴ 70
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1
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759
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 10 months ago by 43k • written 10 months ago by • 0
1
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0
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405
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RUVg spike-in assumption global expression
RUVSeq RUVnormalize
10 months ago Erdi ▴ 10
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0
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397
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determine k during RUVSeq
RUVSeq RUVnormalize
12 months ago Ειρήνη • 0
2
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9
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1.4k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 months ago by 68k • written 12 months ago by • 0
3
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6
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1.3k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
13 months ago nhaus ▴ 70
3
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2
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732
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
15 months ago Shaimaa Gamal • 0
4
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3
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922
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 15 months ago by 52k • written 15 months ago by • 0
2
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3
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855
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 15 months ago by 68k • written 15 months ago by • 0
2
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5
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1.1k
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Batch-resolved visualization after RUVg normalization?
RUVSeq
16 months ago ctlong • 0
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6
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1.2k
views
Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 17 months ago by 43k • written 18 months ago by • 0
5
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9
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2.4k
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Batch correction and repeated measures
RUVSeq sva limma
updated 13 months ago by 52k • written 19 months ago by ▴ 10
3
votes
5
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1.8k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
0
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4
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1.2k
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DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
21 months ago anne.hoffrichter • 0
3
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12
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2.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
1
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2
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1.3k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
2.1 years ago AZ ▴ 30
0
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0
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630
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.1 years ago Luca • 0
1
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2
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1.6k
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.1 years ago garbuzov • 0
3
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6
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1.6k
views
RUVr batch correction doubling number of DEGs
DESeq2 RUVSeq
2.3 years ago • updated 2.1 years ago Zainab ▴ 20
0
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1
reply
1.1k
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RUV with K more than 1.
RUVSeq
updated 2.3 years ago by ★ 4.8k • written 2.3 years ago by ▴ 10
0
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3
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1.4k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
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0
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713
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RUVg for SNAP-ChIP ?
RUVSeq
2.4 years ago Bogdan ▴ 670
0
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1
reply
948
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.8 years ago Tongjun • 0
0
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4
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3.3k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
2.9 years ago Mohamed ▴ 30
1
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7
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2.2k
views
RUVseq, DESeq2, and different codesets for nanostring data
RUVSeq DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 60
1
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1
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1.0k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 20
2
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7
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2.2k
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CPM after RUVseq
RUVSeq CPM Normalization
3.0 years ago Jess • 0
0
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5
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5.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
1
vote
1
reply
1.1k
views
Incorporating RUVg results into ImpulseDE2 model
ImpulseDE2 ImpulseDE ERCC RUVSeq
3.6 years ago • updated 3.5 years ago Mallory ▴ 10
1
vote
5
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2.4k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 9 months ago by ▴ 70 • written 3.9 years ago by ▴ 60
2
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6
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5.8k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.9 years ago reganhayward • 0
2
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2
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1.9k
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How to retain metadata after running RemoveBatchEffect() after RUVSeq to format PCA plot?
plotPCA DESeq2 RUVSeq removebatcheffect()
4.0 years ago elizabethe819 • 0
0
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0
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866
views
Identification of the empirical control genes to use RUVg in order to correct more than two batches
RUVSeq
4.1 years ago bioinfc • 0
0
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7
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2.2k
views
RUVSeq package for adjusting two variables of interest
RemoveUnwantedVariation RNA-sequencing RUVSeq
updated 4.3 years ago by ▴ 980 • written 4.3 years ago by • 0
5
votes
6
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2.1k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 20
0
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2
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1.7k
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
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7
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24k
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DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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0
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881
views
"Frozen" RUVseq normalization
RUVseq machine learning
5.0 years ago acquaviva.massimo • 0
2
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6
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1.8k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
2
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4
replies
2.7k
views
full confounding between batch and treatment effects
batch effects limma batch-correction RNAseq RUVseq
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
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3
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1.3k
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unable to find inherited method inRUVG
ruvseq RUVSeq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
1
vote
4
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2.8k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.5 years ago Arindam ▴ 80
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2
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2.1k
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Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
RUVseq
updated 5.6 years ago by ▴ 980 • written 5.6 years ago by • 0
1
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1
reply
1.7k
views
Using RUVs with known batches
ruvseq deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 30
0
votes
1
reply
947
views
[DESeq2] sequin [ANAQUIN] correction, too many factors in model
deseq2 ruvseq anaquin sequins
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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0
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1.1k
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Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
5.9 years ago garbuzov • 0
0
votes
2
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3.1k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 5.9 years ago by ▴ 980 • written 6.1 years ago by • 0
2
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4
replies
3.0k
views
Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 6.0 years ago by ▴ 980 • written 6.0 years ago by ▴ 260
0
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0
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1.1k
views
RUVseq: Use of known controls with RUVg
RUVseq
6.0 years ago bio.erikson • 0
50 results • Page 1 of 1
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Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…
Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
It is in ! It just took longer than planned :) ... aaaand now that I added the heatmap in I realize lits of genes really do not look like t…
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Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
Answer: limma correction for tumor purity
Answer: limma correction for tumor purity
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