Showing : RUVSeq • reset
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Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 6.4 years ago by ▴ 980 • written 6.5 years ago by • 0
2
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4
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3.2k
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Upper-quartile normalization before RUVg normalization?
RUVSeq
updated 6.4 years ago by ▴ 980 • written 6.4 years ago by ▴ 270
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1.2k
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RUVseq: Use of known controls with RUVg
RUVseq
6.5 years ago bio.erikson • 0
1
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3
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2.9k
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Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq ruvseq RUVs DESEq2 deseq2
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 680
4
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4
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3.1k
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RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 680
0
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1
reply
1.5k
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merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 50
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1.7k
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Adding labels to pca plot from EDASeq package 'plotPCA'
ruvseq edaseq pca
6.9 years ago kbobowik • 0
0
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8
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2.9k
views
normalized counts from RUVg run: is further library size normalization needed?
RUVSeq
updated 6.9 years ago by ▴ 980 • written 6.9 years ago by ▴ 10
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2
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2.6k
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determine k during RUVSeq
ruvseq
updated 6.9 years ago by ▴ 980 • written 7.0 years ago by ▴ 10
1
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9
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3.5k
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EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 7.1 years ago by ▴ 980 • written 7.1 years ago by ▴ 10
2
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4
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3.0k
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Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 3 months ago by • 0 • written 7.2 years ago by • 0
2
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3
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2.0k
views
Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by • 0
2
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2
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2.5k
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RUVg with differential transcript expression?
ruvseq sleuth
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by • 0
7
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2
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4.1k
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Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2 ruvseq spike-in time course time series
updated 7.8 years ago by ▴ 980 • written 7.8 years ago by ▴ 20
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3
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2.4k
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How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2 ruvseq rna-seq batch effect
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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1
reply
2.0k
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Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.9 years ago by ▴ 980 • written 7.9 years ago by ▴ 10
3
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7
replies
3.0k
views
Batch effects between controls
batch-effect ruvseq
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 10
0
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2
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2.6k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 8.0 years ago by ▴ 980 • written 8.0 years ago by ▴ 50
0
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1
reply
2.7k
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RUVseq: How to implement to more complex time-course model?
ruvseq deseq2 model.matrix confounders
updated 8.2 years ago by ▴ 980 • written 8.2 years ago by ▴ 10
2
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9
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3.5k
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Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 8.2 years ago by ▴ 980 • written 8.2 years ago by ▴ 90
1
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3
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3.2k
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Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV ruvseq ruvr ruvnormalize single cell
8.2 years ago Nik Tuzov ▴ 90
0
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1
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1.2k
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RNAseq Analysis using RUVs
rnaseq ruvseq r
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by • 0
0
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1
reply
1.9k
views
How to generate heatmap for three groups
rnaseq ruvseq heatmap
updated 8.3 years ago by 68k • written 8.3 years ago by • 0
2
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1
reply
1.6k
views
Decide normalisation method in RUVseq for RNAseq data
edger ruvseq rnaseq normalization ruvnormalize
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by • 0
5
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4
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3.1k
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Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
deseq2 ruvseq
updated 8.4 years ago by ▴ 980 • written 8.4 years ago by ▴ 10
2
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3
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2.6k
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How to determine a set of empirical control 'genes' using RUVSeq
RUVSeq
updated 3.3 years ago by ▴ 30 • written 8.6 years ago by • 0
0
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1
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2.8k
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Can FPKM or TPM values be used as RUVs input ?
ruvseq ruvg ruv
updated 8.7 years ago by ▴ 980 • written 8.8 years ago by • 0
0
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1
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1.5k
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Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
dexseq ruvseq rnaseq
updated 8.7 years ago by ▴ 980 • written 8.8 years ago by ▴ 110
1
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1
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1.5k
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Raw read count Vs EdgeR normzlized read count for RUVg normalization
rnaseq ruvseq normalization
updated 8.9 years ago by ▴ 980 • written 8.9 years ago by ▴ 40
0
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4
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3.2k
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DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
8.9 years ago j.viana • 0
0
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5
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2.1k
views
Can Normalized cpm values be used as RUVs input
rnaseq ruvseq
updated 9.1 years ago by ▴ 980 • written 9.1 years ago by • 0
0
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6
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3.9k
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How to use RUVseq with voom-limma for differential expression analysis?
ruvseq limma voom
updated 9.1 years ago by ▴ 980 • written 9.1 years ago by • 0
4
votes
16
replies
9.1k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 19 months ago by • 0 • written 10.4 years ago by ▴ 160
1
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4
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3.1k
views
RUVseq control genes - invalid subscript type 'list'
ruvseq
9.3 years ago eteleeb ▴ 10
2
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1
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2.1k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq RUV ruvnormalize ruvg
9.3 years ago anthonycolombo60 • 0
2
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6
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3.6k
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RUVSeq DE analysis for data with replicate samples and 4 conditions
RUVSeq
updated 9.3 years ago by • 0 • written 10.1 years ago by ▴ 40
1
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2
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1.4k
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RUVSeq and Generalised Linear Mixed Model
ruvseq
updated 9.3 years ago by ▴ 980 • written 9.3 years ago by ▴ 10
2
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6
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2.1k
views
effect of polyploidy level on RUVs normalisation
normalization ruvseq ruvnormalize ruvs eda
9.5 years ago thomas.wolfe • 0
1
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2
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2.3k
views
RUVSEq and VSD integration
deseq2 ruvseq covariates continuous vsd
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 10
4
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5
replies
3.3k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
2
votes
2
replies
1.9k
views
Paired analysis and batch effects ?
ruvseq sva edger
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 10
1
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2
replies
2.7k
views
RUVg or RUVs
ruvseq
updated 9.7 years ago by ▴ 10 • written 9.7 years ago by ▴ 80
1
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1
reply
2.1k
views
RUVSeq installation problems
RUVSeq bioconductor biocinstaller
updated 9.7 years ago by ▴ 980 • written 9.7 years ago by • 0
2
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4
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2.4k
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RUVseq design matrix for first pass of edger
ruvseq
written 9.8 years ago by ▴ 80
2
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4
replies
4.9k
views
Number of co-variables k in RUVSeq (RUVr)
rnaseq ruvseq RUVr edgeR
9.9 years ago David R ▴ 90
1
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3
replies
2.1k
views
RUVseq coefficients for unwanted variance in design matrix
ruvseq edger deseq2
9.9 years ago tonja.r ▴ 80
1
vote
2
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2.8k
views
RUVseq using RUVg most non-differential expressed genes
ruvseq
updated 9.9 years ago by ▴ 980 • written 9.9 years ago by ▴ 80
6
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7
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4.8k
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RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
9.9 years ago tonja.r ▴ 80
0
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5
replies
2.9k
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RUVseq for microRNAs
ruvseq ruv microrna
10.2 years ago sergio.espeso-gil • 0
2
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12
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3.4k
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LAPACK/BLAS error with edgeR GLM
glm edger lapack segfault ruvseq
10.2 years ago Mark.Rogers • 0
108 results • Page 2 of 3
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Comment: gene Set with high AUC score but no cells assigned to cell type by eja.hdrer33ge.r.m • 0
Understanding complex data results like those from AUCell can be challenging. For easier analysis and better data management on the go you …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
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