Showing : Rnaseq • reset
0
votes
3
replies
1.6k
views
DeSeq2- design experiment
rnaseq degseq
8.0 years ago laksharikrish • 0
0
votes
3
replies
1.1k
views
Dseq single factor and 4 levels experiment design
rnaseq deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
5
votes
1
reply
3.2k
views
Difference between heatmap using Euclidian distance and Poisson distance
deseq2 euclidean sample distance rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
0
votes
0
replies
794
views
comparison of expression between orthologous species
rnaseq differential gene expression
8.0 years ago laksharikrish • 0
1
vote
2
replies
718
views
DE Analysis strategies for designs that are "not full rank"
deseq2 rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
11
votes
3
replies
4.3k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
28
votes
7
replies
14k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 2.0 years ago by ▴ 10 • written 8.0 years ago by ▴ 40
5
votes
2
replies
1.7k
views
DESeq2 contrast give different results for same comparison using standard analysis
rnaseq deseq2
8.0 years ago Letícia ▴ 10
3
votes
0
replies
2.0k
views
What's the correct way to normalize HTseq files with TCGAbiolinks
normalization R rnaseq bioconductor
8.0 years ago eshelden ▴ 40
0
votes
2
replies
1.8k
views
creating design and count matrix for rna-seq differential expression
limma rnaseq edger
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
2
votes
1
reply
2.0k
views
SGSeq error on getBamInfo
SGSeq getBamInfo RNASeq
updated 8.0 years ago by ▴ 260 • written 8.0 years ago by ▴ 40
1
vote
11
replies
8.5k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
8.0 years ago tanyabioinfo ▴ 30
1
vote
3
replies
1.6k
views
DESeq: large difference in number of replicates per condition
deseq2 rnaseq differential expression
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
2
votes
4
replies
1.7k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 8.0 years ago by ★ 13k • written 8.0 years ago by ▴ 90
0
votes
1
reply
3.6k
views
NA values of count matrix in class DESeqDataSet
rnaseq recount
8.0 years ago maleknias • 0
25
votes
7
replies
13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 20
10
votes
6
replies
5.5k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 8.1 years ago by ▴ 110 • written 10.4 years ago by 21k
0
votes
1
reply
2.0k
views
DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
votes
1
reply
904
views
differentially expressed genes form RSEM genes data
rnaseq edgeR
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 20
0
votes
1
reply
1.7k
views
RNA-Seq DEG analysis questions
rnaseq deg
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
8
votes
3
replies
2.5k
views
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
edgeR rnaseq limma independent filtering
8.1 years ago Robert Castelo ★ 3.4k
0
votes
0
replies
1.2k
views
Combined strand specific and unstranded samples
strand rnaseq differential gene expression batch effect counts
8.1 years ago lirongrossmann ▴ 80
5
votes
2
replies
4.6k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.5 years ago by • 0 • written 8.1 years ago by • 0
0
votes
1
reply
1.9k
views
Set rnaseq locial flag during GSVA
gsva rnaseq tpm
updated 8.1 years ago by ★ 3.4k • written 8.2 years ago by • 0
0
votes
2
replies
733
views
R script problem
R rnaseq bioconductor
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
2
votes
2
replies
1.5k
views
Why does total unique map not equal to library size?
htseqcounts star rnaseq
8.1 years ago Ahdee ▴ 60
0
votes
7
replies
9.6k
views
Regarding scRNA seq vs Bulk RNA seq
single cell rnaseq
updated 8.1 years ago by ▴ 10 • written 8.1 years ago by • 0
2
votes
3
replies
3.8k
views
DESEq2 p-values weird distribution under the H0 and fdrtool
rnaseq deseq2 fdrtool differential gene expression
8.1 years ago tcalvo ▴ 100
1
vote
1
reply
2.6k
views
High variation among biological replicates. Options for correction during DE analysis
rnaseq
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
3
votes
3
replies
8.7k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.2 years ago by 21k • written 8.2 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
4
votes
8
replies
2.7k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger DGE no replicates
8.2 years ago Stefany Solano • 0
5
votes
4
replies
2.1k
views
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
limma rnaseq rna-seq model-matrix multiple factor design
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
7
votes
3
replies
3.9k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
3
replies
1.9k
views
Is the CPM filtering method from NOISeq unsupervised?
rnaseq de analysis gene filtering noiseq
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 50
2
votes
1
reply
1.5k
views
Read normalization in derfinder
derfinder normalization rnaseq
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Polyester - creating simulated reads based on raw count matrix
polyester rnaseq simulation
8.2 years ago sseo2 • 0
0
votes
2
replies
1.9k
views
ggplots gives errors
rnaseq ggplot2
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by • 0
3
votes
6
replies
23k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
8.2 years ago nikmehr22 • 0
2
votes
1
reply
1.3k
views
Derinder options (species, annotations style)
derfinder rnaseq differential expression
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Tools for classifying reads from xenograft samples?
rnaseq xenograph
8.2 years ago alakatos ▴ 130
1
vote
3
replies
2.8k
views
Annotate gene counts
annotation RNASeq annotationdbi
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
votes
1
reply
1.7k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
votes
5
replies
2.8k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
8.2 years ago Jens Preussner ▴ 30
0
votes
1
reply
2.2k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
0
votes
5
replies
3.6k
views
Load saved RangedSummarizedExperiment as Deseq2 dataset
deseq2 hdf5 rangedsummarizedexperiment rnaseq
8.2 years ago Jakob Petereit • 0
3
votes
11
replies
4.4k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 30
3
votes
7
replies
3.7k
views
deseq2 complex time course data with out replicates
deseq2 timecourse rnaseq
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by • 0
1
vote
3
replies
2.6k
views
[DESeq2] time-course Experimental design
rnaseq deseq2 time-course
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 10
1,409 results • Page 16 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
Awards • All
Popular Question to Michael Love 43k
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Locations • All
France, 14 minutes ago
United States, 15 minutes ago
Barcelona, Spain, 27 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1340 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6