Showing : Rnaseq • reset
7
votes
7
replies
9.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 6.9 years ago by • 0 • written 8.4 years ago by ▴ 50
0
votes
3
replies
1.1k
views
RNA seq analysis
rnaseq machine learning
6.9 years ago marak • 0
2
votes
4
replies
2.1k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 60
0
votes
2
replies
1.6k
views
feature reduction using machine learning
rnaseq machine learning feature selection
updated 6.9 years ago by ▴ 420 • written 6.9 years ago by • 0
2
votes
2
replies
2.4k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 10
1
vote
4
replies
1.8k
views
RNA-seq analysis using R
limma rnaseq convert R
updated 2.5 years ago by 53k • written 6.9 years ago by ▴ 10
2
votes
6
replies
2.6k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq topgo go enrichment
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
6
votes
7
replies
2.6k
views
Normalization for small non-coding RNA
TMM deseq2 smallrna rnaseq
updated 6.9 years ago by ▴ 510 • written 6.9 years ago by ▴ 90
0
votes
0
replies
1.3k
views
ASpli Package: Problem with readCounts() function, no Junctions analysed.
rnaseq alternative splicing ASpli
6.9 years ago nicolas.guyon2 • 0
3
votes
3
replies
2.4k
views
GZIP ERROR:-2 using featureCounts (Subread)
software error rnaseq
6.9 years ago gbreard ▴ 10
0
votes
4
replies
1.4k
views
DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
6.9 years ago Maithê Barros ▴ 10
0
votes
1
reply
740
views
Issue with normalization in DESeq2
deseq2 normalization rnaseq
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
0
votes
3
replies
1.0k
views
Pre-filtering results influence on downstream analysis
deseq2 rnaseq
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 20
3
votes
3
replies
1.7k
views
How to decide whether a variate should be in the model or not
deseq2 rnaseq
updated 2.6 years ago by 43k • written 6.9 years ago by ▴ 20
4
votes
7
replies
3.1k
views
Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
deseq2 design model rnaseq multiple factor levels
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
0
votes
0
replies
1.4k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
6.9 years ago Mithil Gaikwad • 0
4
votes
2
replies
2.1k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 6.9 years ago by ★ 13k • written 6.9 years ago by ▴ 60
0
votes
7
replies
2.4k
views
DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
6.9 years ago bharata1803 ▴ 60
0
votes
4
replies
1.5k
views
DESeq2 MA plot normalisation Issue
deseq2 normalization maplot rnaseq
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
3
replies
1.8k
views
Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
2
replies
939
views
Help with edgeR code - RNA-Seq Differental Gene Expression
edger rnaseq
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
2
votes
14
replies
3.0k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 30
0
votes
1
reply
1.6k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
7
votes
9
replies
4.4k
views
Dispersion fit and p-value distributions
deseq2 rnaseq fdrtool
updated 7.0 years ago by ★ 7.9k • written 7.0 years ago by ▴ 140
0
votes
1
reply
1.4k
views
Normalization and Quality Control for Multiple scRNAseq Data Sets
normalization rnaseq genetics batch effect dropout
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
0
votes
3
replies
1.6k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
7.0 years ago Ben ▴ 50
0
votes
4
replies
1.2k
views
how to make gene cluster from RNA-Seq counts?
deseq2 rnaseq R
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
4
replies
1.4k
views
DESeq2 design with multiple factors
rnaseq deseq2 multiple factor design
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
vote
5
replies
3.3k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
7.0 years ago hamza_karakurt ▴ 60
2
votes
7
replies
3.2k
views
How to block for a subject in a 2 factor design formula
deseq2 differential gene expression rnaseq
7.0 years ago Onyi Ukay • 0
0
votes
2
replies
1.7k
views
DESeq2 got stuck for one night, restarting?
deseq2 rnaseq
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 20
1
vote
1
reply
2.5k
views
EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 30
0
votes
6
replies
3.0k
views
Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
rnaseq rsem deseq2
7.0 years ago loliveira • 0
8
votes
8
replies
8.8k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 60
2
votes
2
replies
1.2k
views
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
0
votes
2
replies
1.4k
views
Limma analysis combining twins pairs and unpaired controls
limma twin analysis rnaseq
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
2
votes
5
replies
3.0k
views
Visualise and remove batch effects in DESeq2
deseq2 rnaseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
3
votes
4
replies
1.9k
views
edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
0
votes
2
replies
1.7k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
2
replies
1.6k
views
Problem running (loading) systemPipeR package after downloading
systemPipeR rnaseq
7.1 years ago rj.innet • 0
3
votes
5
replies
1.7k
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
vote
1
reply
1.8k
views
Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
single-cell rnaseq mitochondria
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
4
votes
5
replies
2.0k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
1
vote
0
replies
1.4k
views
Evaluating Hub genes in WGCNA and role of using Signed network
rnaseq WGCNA
7.2 years ago dorothy.jrobbert ▴ 30
0
votes
3
replies
849
views
A few up-regulated genes using an extravagant number of reads - effect on DE analysis
rnaseq deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
2
votes
4
replies
9.8k
views
Adding gene names (or symbols) in my DESeq result
rnaseq gene names deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
3
votes
9
replies
3.4k
views
DESeq2 Normalized Counts for Mfuzz
deseq2 rnaseq mfuzz
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 50
0
votes
3
replies
1.8k
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 670
3
votes
2
replies
3.7k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 7.2 years ago by 53k • written 7.3 years ago by • 0
2
votes
4
replies
1.9k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger cpm non-specific filtering rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 840
1,409 results • Page 12 of 29
Recent ...
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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