Showing : RNAseq • reset
4
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4
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1.8k
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Setting contrasts in limma where null hypothesis is that Test = 2 x Control
differential gene expression limma rnaseq design and contrast matrix limma voom
9.7 years ago stuart ▴ 10
2
votes
4
replies
2.1k
views
Bowtie % mapped reads for DGE
Bowtie quasr rnaseq
updated 9.7 years ago by ★ 1.6k • written 9.7 years ago by ▴ 10
11
votes
14
replies
5.0k
views
Setting up the Design Matrix
rnaseq edgeR multiple factor design design matrix
9.7 years ago Yogender Gowtham ▴ 20
3
votes
5
replies
8.5k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna rnaseq R bioconductor
updated 9.8 years ago by ★ 3.0k • written 9.8 years ago by ▴ 30
2
votes
4
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3.0k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
9.8 years ago bioprog • 0
6
votes
2
replies
13k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
2
votes
2
replies
1.1k
views
EdgeR does not change when swap the tissue column
edger rnaseq R
updated 9.8 years ago by 53k • written 9.8 years ago by • 0
2
votes
1
reply
3.8k
views
DESeq2 with multiple conditions
deseq2 rnaseq
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 60
0
votes
2
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1.4k
views
Further analysis of gene expression data
limma voom rnaseq
updated 9.8 years ago by ★ 29k • written 9.8 years ago by ▴ 60
0
votes
5
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5.4k
views
Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixe…
limma maanova rnaseq
12.3 years ago • updated 3.8 years ago Gordon Smyth 53k
0
votes
1
reply
1.4k
views
UPC RNA-Seq individual samples
scan.upc upc rnaseq
updated 9.8 years ago by ▴ 600 • written 9.8 years ago by ▴ 30
1
vote
1
reply
4.8k
views
Statistical power of limma vs mixed model approach to analyze microarray and differential proteomics/peptidomics experiments and Poisson/binomial mix…
RNASeq Microarray GO limma edgeR DESeq RNASeq Microarray GO limma edgeR DESeq
updated 9.8 years ago by 53k • written 12.3 years ago by ▴ 60
3
votes
5
replies
2.5k
views
How to handle mix of samples from the same subject and from different subjects during differential expression analysis of RNA-seq using GLMs?
rnaseq rna-seq differential gene expression differential expression edger
updated 9.8 years ago by ★ 7.9k • written 9.8 years ago by ▴ 70
0
votes
1
reply
1.5k
views
RNA-Seq Read Counts for SCAN.UPC
scan.upc rnaseq
updated 9.8 years ago by ▴ 600 • written 9.8 years ago by ▴ 30
0
votes
5
replies
2.4k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 9.8 years ago by ▴ 400 • written 9.8 years ago by • 0
0
votes
0
replies
1.7k
views
Technical Replicates and RUVs Normalisation
rnaseq ruvnormalize normalization technical replicates
9.9 years ago thomas.wolfe • 0
2
votes
4
replies
4.9k
views
Number of co-variables k in RUVSeq (RUVr)
rnaseq ruvseq RUVr edgeR
9.9 years ago David R ▴ 90
2
votes
4
replies
1.4k
views
Big p-value/adj p-value with quite good read count
rnaseq voom limma
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 60
6
votes
11
replies
4.9k
views
edgeR on extremely large dataset
edgeR rnaseq
9.9 years ago martiningi ▴ 40
3
votes
2
replies
1.3k
views
Non-DGE genes from Limma
limma rnaseq microarray
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 60
2
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6
replies
5.1k
views
DESeq2 very slow with many samples
rnaseq deseq2
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
22
votes
13
replies
30k
views
gene dispersion, what does it mean?
gener rnaseq
updated 2.6 years ago by 53k • written 9.9 years ago by ▴ 80
5
votes
5
replies
3.2k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing rnaseq microarray
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 30
1
vote
12
replies
2.6k
views
How to find the differentially expressed genes for paired tumor normal samples without any biological replicates?
rnaseq deseq2
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
12
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6
replies
4.1k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq deseq2 edger
9.9 years ago martiningi ▴ 40
1
vote
6
replies
10k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq r biomart
updated 9.9 years ago by ★ 2.1k • written 9.9 years ago by ▴ 40
3
votes
2
replies
4.3k
views
Limma get all DE genes or filter by logFC
limma microarray rnaseq
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 60
0
votes
5
replies
2.0k
views
Mapping short reads to gene IDs in GPL9115
rnaseq EST gene Id
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 60
11
votes
1
reply
18k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 20
2
votes
2
replies
1.0k
views
Deseq2 using principle components on raw or log normalized counts as covariates
deseq2 rnaseq normalization
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
2
votes
6
replies
2.1k
views
edgeR_robust: where are moderately expressed genes?
edger rnaseq microrna
updated 9.9 years ago by ★ 29k • written 9.9 years ago by • 0
0
votes
0
replies
2.3k
views
Job: Bioinformatics Data Analyst - IMP/IMBA Vienna
chipseq atac-seq gro-seq bsseq rnaseq Job
10.0 years ago Jaritz,Markus ▴ 20
0
votes
1
reply
1.2k
views
RNAseq with two conditions - need help!
rnaseq deseq2 newbie
updated 10.0 years ago by 43k • written 10.0 years ago by • 0
0
votes
1
reply
2.9k
views
Input file of NGS data for Pathview
rnaseq pathview data visualization
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 10
11
votes
11
replies
4.2k
views
Different results in edgeR using simple vs GLM
edger glm rnaseq
10.0 years ago dietahanson ▴ 30
0
votes
0
replies
2.1k
views
Job: PhD Studentship: Genome-scale analysis of host-pathogen interactions
rnaseq single cell bioinformatics R epigenomics Job
10.0 years ago Garry Myers • 0
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 10.0 years ago by ▴ 650 • written 10.0 years ago by ▴ 110
0
votes
1
reply
1.2k
views
DESeq2 Contrast and Design Matrix Question: 4 Experimental Factors
deseq2 rnaseq
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 60
0
votes
1
reply
4.1k
views
maSigPro help- p. vector error
RNASeq maSigPro a4 RNASeq maSigPro a4
updated 10.0 years ago by ▴ 90 • written 11.7 years ago by ★ 13k
0
votes
5
replies
1.5k
views
Comparing sets of differentially expressed genes
deseq2 rnaseq statistics
10.0 years ago sunkid • 0
3
votes
5
replies
12k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
10.0 years ago nickbern92 • 0
3
votes
6
replies
2.7k
views
DESEq2 paired-sample comparison
rnaseq deseq2 formulafullmodel
10.0 years ago alifar76 • 0
1
vote
0
replies
1.9k
views
Job: PhD Student in Computational Biology
differential gene expression rnaseq riboseqr computational biology Job
10.0 years ago Bernd Fischer ▴ 550
3
votes
5
replies
5.3k
views
plotMDS in edgeR
edger rnaseq
written 10.0 years ago by ▴ 30
3
votes
3
replies
1.8k
views
edgeR contrast formulation question
edger rnaseq differential expression
updated 10.0 years ago by ★ 7.9k • written 10.0 years ago by • 0
2
votes
3
replies
1.7k
views
Technical and biological replates in BitSeq
BitSeq bitseq rnaseq
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by ▴ 300
0
votes
0
replies
2.2k
views
Job: Bioinformatics Analyst at University of Cambridge, Cancer Research UK Cambridge Institute
job jobs rnaseq chipseq dnaseq Job
10.1 years ago Rory Stark ★ 5.2k
2
votes
3
replies
1.8k
views
negative values for trended dispersion with edgeR
rnaseq estimatedispersions edgeR
updated 10.1 years ago by ▴ 900 • written 10.1 years ago by ▴ 20
0
votes
0
replies
2.1k
views
Job: Research Scientist in Bioinformatics/Statistical Genomics, Max Planck Institute, Nijmegen, Netherlands
job rnaseq rna-seq genomics data integration Job
10.1 years ago clyde.francks • 0
3
votes
3
replies
2.4k
views
edgeR analysis of effect of treatments within time points
edger rnaseq
updated 10.1 years ago by ▴ 900 • written 10.1 years ago by • 0
1,409 results • Page 22 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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