Showing : RNAseq • reset
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DESeq2 design formula/experiment table help
rnaseq differential gene expression deseq2 r
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
2
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3
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3.1k
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How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
8.5 years ago aec ▴ 90
1
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2
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3.6k
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Tutorial for RNA-Seq Data Analysis
rnaseq data analysis tutorial workflows differential gene expression
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
12
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6
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3.3k
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How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger differential gene expression rnaseq
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 20
2
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6
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1.8k
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How to do multivariate glmFit analysis of RNA-seq with edgeR
limma edger rnaseq
8.5 years ago mousheng xu ▴ 10
5
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7
replies
12k
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threshold to filter lowly expressed genes
edger rnaseq
updated 21 months ago by • 0 • written 8.6 years ago by • 0
0
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3
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1.8k
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Nugen adapter in RNA seq
rnaseq
8.6 years ago tg369 ▴ 10
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0
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1.0k
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Network Export error and TOM object save error
rnaseq
8.6 years ago m.azhar ▴ 10
0
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0
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3.0k
views
How to normalize-transform rsem.genes.results of TCGA RNA-seq v2?
tcga rnaseq rsem R normalization
8.6 years ago panagiotis.mokos ▴ 40
3
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5
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12k
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DESeq2 Following RSEM
deseq2 rnaseq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
1
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0
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1.3k
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network.Rdata file into TOM file error
rnaseq
8.6 years ago m.azhar ▴ 10
2
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3
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2.4k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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1
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1.9k
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intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
2
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3
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2.6k
views
edgeR ANOVA-like analysis
edger rnaseq anova
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
1
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2
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1.9k
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Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR RNAseq experimental design glm
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
3
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12
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4.7k
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Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga rnaseq glmnet voom deseq2
8.6 years ago panagiotis.mokos ▴ 40
1
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8
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3.9k
views
[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2 outliers RNAseq differential gene expression
8.6 years ago cajawe • 0
0
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1
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1.6k
views
memory allocation error
rnaseq
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 10
0
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18
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7.8k
views
WGCNA error in network construction ?
microarray rnaseq
8.6 years ago m.azhar ▴ 10
0
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4
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3.0k
views
Normalization and transformation of RNA-seq raw data for regularized linear regression models
rnaseq glmnet limma voom deseq2
8.6 years ago panagiotis.mokos ▴ 40
5
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8
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5.4k
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 8.6 years ago by ▴ 40
1
vote
7
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3.9k
views
Linear regression model in RNA seq
deseq2 limma R rnaseq
8.6 years ago Karl Fees ▴ 10
6
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7
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5.5k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 90
2
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1
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1.6k
views
DESeq2 for read count input from 2 different NGS platforms
rnaseq deseq2
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 60
0
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0
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2.0k
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Problem when using topGO for RNAseq data: The number of annotated genes for GO terms changes according to the number of genes in the gene-background-…
topGO gene ontolology rnaseq
8.6 years ago colaneri ▴ 30
9
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4
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4.3k
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GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 30
3
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1
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1.5k
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RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2 deseq rnaseq
8.6 years ago ysdel ▴ 40
3
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3
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1.4k
views
limma decideTests: only p-value less than (but not equal to) alpha are flagged as significant
limma edger significance rnaseq
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 20
4
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6
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2.0k
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Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
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0
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1.3k
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cummeRbund error dealing with cuffdiff results
rnaseq cummerbund R software error
8.6 years ago wastdc • 0
1
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1
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1.6k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
5
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3
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8.2k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 40
3
votes
3
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2.2k
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Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
1
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4
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2.3k
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Can edgeR be used on GO terms?
edger go rnaseq
8.6 years ago y.zhang36 • 0
1
vote
13
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5.4k
views
Similar to Tukey Post hoc after ANOVA
rnaseq multiple comparisons post hoc deseq2
9.4 years ago • updated 8.6 years ago laianavarromartin ▴ 20
2
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3
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2.4k
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Issues with DEXSeq: rows did not converge in beta
rnaseq dexseq
8.7 years ago Konstantin Okonechnikov ▴ 40
0
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1
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1.8k
views
IRanges object from count matrix
genomicranges iranges featurecounts counts rnaseq
updated 8.7 years ago by 16k • written 8.7 years ago by ★ 1.5k
3
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11
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12k
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How to interpret plotBCV plots in edgeR
rnaseq edger
8.7 years ago davide.bau • 0
0
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0
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1.5k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
8.7 years ago Ryan C. Thompson ★ 7.9k
3
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6
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1.8k
views
Possible approach of compare/interpret RNA-Seq results with microarray gene expression describing the same phenotype
microarray rnaseq DEgenes meta-analysis limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 840
3
votes
5
replies
5.9k
views
How to deal with low-depth RNA-Seq within DESeq2 or edgeR
rnaseq normalization differential gene expression edger deseq2
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by ▴ 90
0
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1
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1.4k
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DESeq2 - differentially expressed genes for each sample
deseq2 rnaseq
8.7 years ago norty89 • 0
2
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9
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2.8k
views
Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
8.7 years ago j.baldauf • 0
4
votes
9
replies
4.3k
views
WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
WGCNA similarity correlation bioconductor rnaseq
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by ▴ 40
0
votes
1
reply
1.5k
views
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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1.7k
views
plot Heatmap after the use of "Interaction" within DESeq2
rnaseq deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 40
1
vote
1
reply
724
views
RNA-seq workflow at the gene level - "colSums(assay(se))" command ?
RNAseq Summarized experiment
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
2
votes
5
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1.6k
views
Including novel transcripts and antisense into differential gene expression analysis
edger rnaseq
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
25
votes
37
replies
15k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 840
0
votes
0
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1.2k
views
RNA Seq // QuasR : Error while extracting unmapped reads
quasr quasr error paired-end reads rnaseq
8.8 years ago guillaume.dachy • 0
1,409 results • Page 18 of 29
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Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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