Showing : Rnaseq • reset
0
votes
1
reply
1.2k
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
2
votes
1
reply
1.5k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
6
votes
6
replies
3.5k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.4 years ago svlachavas ▴ 840
1
vote
2
replies
733
views
Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
4.4 years ago fernandogs97 ▴ 10
1
vote
2
replies
883
views
Technical reps
RNASeq DESeq2
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
3
votes
9
replies
8.0k
views
LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
updated 3.7 years ago by • 0 • written 4.4 years ago by • 0
0
votes
3
replies
1.4k
views
DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
1
vote
4
replies
1.5k
views
Need help in running GO analysis
RNASeq R
4.4 years ago Rishav ▴ 20
4
votes
1
reply
3.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 21 months ago by 53k • written 4.4 years ago by ▴ 60
0
votes
4
replies
1.6k
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
4.5 years ago Yuqia • 0
1
vote
6
replies
3.3k
views
The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2 RNASeq
4.5 years ago hequn • 0
1
vote
3
replies
3.2k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4.5 years ago dantasezequiel1 • 0
2
votes
2
replies
3.5k
views
How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR RNASeq
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
1
vote
2
replies
1.6k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
4.5 years ago Torkel • 0
3
votes
4
replies
2.1k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
4.5 years ago hgalmoore • 0
0
votes
1
reply
1.2k
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
0
votes
2
replies
1.4k
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
4.5 years ago annadv • 0
2
votes
5
replies
5.0k
views
DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 2.9 years ago by 43k • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.2k
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 10
0
votes
1
reply
953
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
vote
4
replies
3.5k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 24 months ago by • 0 • written 4.6 years ago by • 0
1
vote
1
reply
1.9k
views
read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
7
votes
12
replies
5.9k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 2.0 years ago by • 0 • written 4.6 years ago by • 0
2
votes
2
replies
1.7k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.6 years ago n.tear ▴ 20
1
vote
0
replies
962
views
Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.6 years ago nageshprabhu.k ▴ 10
2
votes
2
replies
1.5k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
0
votes
0
replies
861
views
Circular RNA
CircularRNA RNASeq RNAseq123
4.7 years ago rpokhre2 • 0
0
votes
4
replies
2.3k
views
DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by • 0
1
vote
1
reply
1.3k
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
2
votes
0
replies
1.4k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.7 years ago Ben ▴ 50
0
votes
2
replies
1.1k
views
Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
1
reply
634
views
Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
2
votes
8
replies
4.1k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 22 months ago by • 0 • written 4.8 years ago by ▴ 20
3
votes
15
replies
4.4k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
3
votes
9
replies
11k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 4.8 years ago by • 0 • written 10.2 years ago by • 0
0
votes
1
reply
834
views
DESeq2 with three factor experimental design
DESeq2 RNASeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
votes
2
replies
1.4k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 4.9 years ago by ▴ 360 • written 4.9 years ago by ▴ 10
0
votes
2
replies
2.0k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.9 years ago harelarik ▴ 60
0
votes
1
reply
2.5k
views
Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
PCAtools biplot DESeq2 RNASeq PCA
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 30
0
votes
3
replies
3.1k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 10
2
votes
3
replies
2.9k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 100
15
votes
3
replies
2.3k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 3.7 years ago by ▴ 30 • written 4.9 years ago by ▴ 90
1
vote
1
reply
1.9k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
0
votes
4
replies
1.4k
views
DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
4.9 years ago dagurim • 0
2
votes
1
reply
978
views
How to extract top DEG and their sample values
DESeq2 RNASeq
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 30
0
votes
2
replies
4.2k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
3
votes
3
replies
3.1k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 60
0
votes
0
replies
1.3k
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
5.0 years ago Laurent Gatto 1.6k
3
votes
4
replies
2.1k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 5.0 years ago by ★ 4.1k • written 5.0 years ago by • 0
0
votes
1
reply
1.3k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1,409 results • Page 8 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
United States, 1 hour ago
The city by the bay, 3 hours ago
United States, 5 hours ago
Pittsburgh, United States, 7 hours ago
United States, 7 hours ago
Traffic: 944 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