Showing : RNASeq • reset
0
votes
9
replies
3.3k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.2 years ago by • 0 • written 8.2 years ago by ▴ 60
1
vote
4
replies
1.6k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
0
votes
0
replies
909
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.2 years ago mch • 0
6
votes
2
replies
2.4k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
0
votes
6
replies
2.4k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.2 years ago erika.maldonado-rosado • 0
0
votes
0
replies
778
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
2.3 years ago Sara • 0
0
votes
2
replies
1.2k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.3 years ago • updated 2.2 years ago Karthik • 0
0
votes
0
replies
772
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.3 years ago Florian • 0
0
votes
0
replies
1.1k
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
2.3 years ago Xinqi • 0
0
votes
0
replies
989
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
2.3 years ago Sara • 0
1
vote
1
reply
1.1k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
7
replies
1.9k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.1 years ago by 53k • written 2.3 years ago by • 0
0
votes
2
replies
897
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
0
votes
1
reply
1.2k
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
3
votes
5
replies
2.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
1
reply
948
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
878
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
1
vote
6
replies
3.8k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
6
votes
7
replies
1.6k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
0
votes
1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.5 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.5 years ago Matteo • 0
4
votes
2
replies
3.8k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
0
votes
3
replies
1.8k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
3
votes
11
replies
5.1k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
2.7 years ago • updated 2.6 years ago Anna ▴ 20
5
votes
9
replies
7.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.9 years ago by ▴ 20
0
votes
1
reply
906
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Anova table edgeR limma
limma RNASeq edgeR
2.7 years ago KATHERINE CHUERE NUNES • 0
1
vote
2
replies
1.2k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
votes
3
replies
1.5k
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
1
vote
3
replies
1.7k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
votes
2
replies
2.6k
views
model matrix not full rank
DESeq2 RNASeq
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
2
votes
3
replies
889
views
RNA seq with edgeR with several factors
RNAseq factors
2.7 years ago Nathalie ▴ 20
0
votes
3
replies
1.4k
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 8 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
0
votes
4
replies
1.9k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
1
vote
1
reply
752
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.7 years ago by 53k • written 2.8 years ago by • 0
3
votes
12
replies
3.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
0
votes
1
reply
788
views
Sample expression calculation in rna seq
Rnaseq
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
1
vote
1
reply
953
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
0
replies
1.0k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.8 years ago Levi • 0
4
votes
8
replies
6.5k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 2.8 years ago by • 0 • written 4.7 years ago by • 0
1
vote
2
replies
1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.8 years ago by • 0
2
votes
4
replies
1.5k
views
limma with or without intercept gives different results
limma rnaseq
2.8 years ago Sydney • 0
1
vote
2
replies
1.9k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
2.8 years ago garbuzov • 0
0
votes
2
replies
1.3k
views
Compare and filter three BAM files
RNAseq 10X
2.8 years ago wt215 • 0
0
votes
5
replies
1.7k
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 2.8 years ago by 53k • written 2.9 years ago by • 0
5
votes
7
replies
1.8k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 2.0 years ago by 53k • written 2.9 years ago by • 0
1,412 results • Page 3 of 29
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Locations • All
Australia, 22 minutes ago
United States, 29 minutes ago
Melbourne, Australia, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Australia, 1 hour ago
Traffic: 1157 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