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RNA-seq
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reset
2
votes
1
reply
2.8k
views
Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma
batch effect
rna-seq
updated 8.5 years ago by
Aaron Lun
★ 29k • written 8.5 years ago by
adscheid3
• 0
0
votes
7
replies
3.1k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 4.1 years ago by
nicolette.sipperly
• 0 • written 8.5 years ago by
urjaswita
▴ 40
1
vote
4
replies
1.6k
views
DESeq2: Tests of log2 differences
deseq2
rna-seq
transcription
dgea
8.5 years ago
fabian
▴ 40
0
votes
1
reply
1.3k
views
can I extract data for subset of cancer types from GSE62944
limma
rna-seq
updated 8.6 years ago by
sina.nassiri
▴ 130 • written 8.6 years ago by
richa_makhijani
• 0
1
vote
5
replies
3.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq
salmon
tximport
limma
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
Endre Sebestyén
▴ 70
3
votes
3
replies
1.6k
views
Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tests
limma
edgeR
sva
RNA-Seq
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
adscheid3
• 0
3
votes
6
replies
2.5k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA
rna-seq
science
bioinformatics
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
Bioinformatician_R
▴ 20
0
votes
1
reply
1.3k
views
Bioconductor RNA-seq bed file read-in/download then wavelet transform
bed files
wavelet
rna-seq
updated 8.6 years ago by
shepherl
4.2k • written 8.6 years ago by
whgsnp
• 0
2
votes
2
replies
2.8k
views
Pairwise differential expression analysis with batch effect using edgeR and SVA
edger
rna-seq
sva
differential expression
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
mpj5142
• 0
5
votes
3
replies
2.8k
views
Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix
limma design matrix
limma
rna-seq
limma voom
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
Jane Park
• 0
1
vote
2
replies
2.5k
views
How to proceed with different degradation levels of RNA-seq samples?
degradation
RNA-seq
variability
differential expression
brain
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
aec
▴ 90
0
votes
1
reply
1.6k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures
txdb
canis familiaris
rna-seq
updated 8.7 years ago by
James W. MacDonald
68k • written 8.7 years ago by
jggomeza
• 0
0
votes
13
replies
2.5k
views
Understanding differences in results with and without setting of pairing factor
DESeq2
deseq2
rna-seq
paired samples
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
solgakar@bi.technion.ac.il
▴ 90
1
vote
3
replies
1.9k
views
How different ploidy affect differential expression analysis with RNA-seq
ploidy
normalization
rna-seq
differential expression
assumption
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
aec
▴ 90
1
vote
5
replies
3.6k
views
Force DESeq2 to use pseudocounts
deseq2
rna-seq
8.7 years ago
manuelw
• 0
1
vote
1
reply
1.3k
views
RIPseeker peak calling parameters for TruSeq Samll RNA stranded library
RIPseeker
RIP
rna-seq
8.7 years ago
ofonov
▴ 10
6
votes
7
replies
5.6k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq
rna-seq
linear model
limma
updated 8.7 years ago by
Aaron Lun
★ 29k • written 8.7 years ago by
Thomas Sandmann
▴ 90
3
votes
3
replies
2.0k
views
Question regarding best bioconductor package for RNA-seq
rna-seq
packages
updated 8.8 years ago by
b.nota
▴ 370 • written 8.8 years ago by
Maximilian
▴ 10
3
votes
2
replies
4.0k
views
Using the ERCC spike as a normalization factor for a custom algorithm
ERCC
rna-seq
edgeR
tmm normalised values
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
what_theheck24
• 0
3
votes
3
replies
2.3k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps
R
bioconductor
rnaseq
rna-seq
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
Walter F. Baumann
▴ 10
9
votes
11
replies
6.3k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport
Kallisto
rna-seq
updated 8.8 years ago by
pablo_garcia05
▴ 20 • written 9.6 years ago by
cguzman.bioinformatics
▴ 10
6
votes
4
replies
2.9k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq
normalization
edgeR
limma
updated 8.8 years ago by
Gordon Smyth
53k • written 8.8 years ago by
juls
• 0
1
vote
1
reply
1.4k
views
RNA-Seq comparisons of various sample
RNA-Seq
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
minie
• 0
1
vote
2
replies
3.2k
views
topGO for Gene Ontology and Gene Set enrichment
topgo
gene ontology
gene set enrichment
rna-seq
bioinformatics
updated 8.9 years ago by
Lluís Revilla Sancho
▴ 760 • written 9.2 years ago by
fromhj304
▴ 10
3
votes
6
replies
2.8k
views
DESeq2 with contaminating cell types
deseq2
rna-seq
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
hughes.drew
▴ 100
0
votes
2
replies
2.8k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown
rna-seq
updated 8.9 years ago by
Alyssa Frazee
▴ 210 • written 8.9 years ago by
Ir
• 0
0
votes
4
replies
2.7k
views
Error: Pathway analysis using Sleuth results
pathview
gage
rna-seq
R
sleuth
8.9 years ago
bioinf
▴ 10
0
votes
0
replies
1.1k
views
Problem annotating with COHCAP 1.16.0 in MacOsX
illimina 450k methylation
RNA-seq
COHCAP
8.9 years ago
IOM
▴ 20
1
vote
1
reply
1.7k
views
Drug datasets for RNA-seq
rna-seq
data
updated 8.9 years ago by
Gordon Smyth
53k • written 8.9 years ago by
bioinformatics
▴ 30
4
votes
9
replies
2.1k
views
RNA-seq analysis edgeR
rna-seq
edger
updated 9.0 years ago by
Ryan C. Thompson
★ 7.9k • written 9.0 years ago by
es874
▴ 20
1
vote
1
reply
853
views
Limma MDS plot donor effect
limma
rna-seq
updated 9.0 years ago by
Aaron Lun
★ 29k • written 9.0 years ago by
es874
▴ 20
2
votes
1
reply
3.7k
views
how to plot PCA for only one of two groups compared or plot three groups at a time
deseq2
bioconductor
rna-seq
pca
updated 9.1 years ago by
Michael Love
43k • written 9.1 years ago by
Mnoon
▴ 20
3
votes
7
replies
2.0k
views
edgeR RNA-seq analysis using glm
edger
rna-seq
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
es874
▴ 20
2
votes
3
replies
3.7k
views
Analysis of RNA-seq time series with edgeR
edger
rna-seq
differential expression
timecourse
time course
updated 9.1 years ago by
Aaron Lun
★ 29k • written 9.1 years ago by
Francesca
• 0
0
votes
0
replies
1.5k
views
Job:
Seeking computational biologists with expertise in RNA-Seq and/or statistics at Immuneering Corporation, Cambridge MA and New York NY
rna-seq
CNS
Neurodegeneration
statistics
computational biology
Job
9.1 years ago
mmartin
▴ 20
1
vote
3
replies
1.4k
views
the output DEGs of limma analyzing RNA-seq data is just 1/3 of those by Tophat-CuffDiff
differential gene expression
voom
limma
RNA-seq
updated 9.1 years ago by
Gordon Smyth
53k • written 9.1 years ago by
boyashuang
• 0
1
vote
5
replies
2.3k
views
How to filter tximport output for edgeR?
tximport
edger
salmon
rna-seq
updated 9.1 years ago by
Michael Love
43k • written 9.1 years ago by
Peter
• 0
8
votes
1
reply
4.4k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma
rna-seq
multi-mapped reads
normalization
microbiome
updated 9.2 years ago by
Steve Lianoglou
★ 13k • written 9.2 years ago by
tealfurn
▴ 30
1
vote
3
replies
3.0k
views
Gene Ontology and Gene Set Enrichment
rna-seq
bioinformatics
gene ontology
gene set enrichment
go
updated 9.2 years ago by
Guangchuang Yu
★ 1.2k • written 9.2 years ago by
fromhj304
▴ 10
2
votes
10
replies
13k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
fromhj304
▴ 10
1
vote
5
replies
5.3k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA
RNA-Seq
updated 9.2 years ago by
Peter Langfelder
★ 3.0k • written 9.2 years ago by
gokce.ouz
▴ 70
2
votes
5
replies
2.1k
views
Differential Gene Expression
deseq2
bioinformatics
rna-seq
Tutorial
updated 9.2 years ago by
Michael Love
43k • written 9.2 years ago by
fromhj304
▴ 10
5
votes
3
replies
3.5k
views
Analyzing RNA-seq data by WGCNA
wgcna
rna-seq
updated 9.2 years ago by
Peter Langfelder
★ 3.0k • written 9.2 years ago by
bram.verstockt
▴ 20
11
votes
8
replies
12k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 9.2 years ago by
Peter Langfelder
★ 3.0k • written 9.2 years ago by
gokce.ouz
▴ 70
1
vote
2
replies
1.8k
views
RNA-seq time series data analysis
RNA-seq
Log-linear
Main effects
updated 9.2 years ago by
Aaron Lun
★ 29k • written 9.2 years ago by
natalia.fghf
• 0
4
votes
4
replies
2.0k
views
Correlation analysis taking into account multiple correlations
edger
rna-seq
correlation
updated 9.2 years ago by
Andrew_McDavid
▴ 280 • written 9.2 years ago by
jhj89
▴ 10
0
votes
3
replies
1.5k
views
Incorporate "batch" information for paired-design ?
RNA-Seq
deseq2
batch effect
9.2 years ago
g.atla
▴ 10
5
votes
3
replies
3.8k
views
Error when calculating DE using the classical approach in edgeR
edgeR
differential expression
rna-seq
updated 9.2 years ago by
Gordon Smyth
53k • written 9.2 years ago by
lynski008
• 0
10
votes
14
replies
10k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2
rna-seq
9.3 years ago
anand_mt
▴ 90
1
vote
0
replies
2.0k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq
rna-seq
preprocessing
gsva
9.3 years ago
t.kuilman
▴ 170
418 results • Page
7 of 9
Recent ...
Replies
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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