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8
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2.0k
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DESeq2 cannot relevel
DESeq2
4.2 years ago
Jorge
• 0
0
votes
1
reply
1.1k
views
Error in flowCore::read.FCS(): Error in uint2double(splitted, endian == "big") : vector
read.FCS
flowCore
4.2 years ago
Rainer
• 0
3
votes
2
replies
5.2k
views
gseGO input list
clusterProfiler
4.2 years ago
leakerb
• 0
0
votes
0
replies
1.5k
views
Job:
Postdoctoral Scientist in Statistical Bioinformatics, WEHI, Melbourne, Australia
JobPosting
4.2 years ago
Yunshun Chen
▴ 900
0
votes
1
reply
1.1k
views
Multiple testing correction for p.scores in FELLA
FELLA
4.2 years ago
sergi.picart
▴ 20
0
votes
3
replies
1.7k
views
ENSEMBL BIOMART INTERFACE DOWN?
biomaRt
updated 4.2 years ago by
Mike Smith
★ 6.6k • written 4.2 years ago by
NVSSJ
• 0
2
votes
5
replies
2.1k
views
DESeq2: error while ploting figure
R
DESeq2
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
bioinformaticssrm2011
• 0
5
votes
3
replies
2.4k
views
DeSeq2 Comparing One group vs Two groups
DESeq2
written 4.2 years ago by
jkanbar
▴ 10
8
votes
0
replies
1.5k
views
News:
Bioconductor 3.14 is Released!
release
Packages
Software
Release
Bioconductor
4.2 years ago
shepherl
4.3k
0
votes
3
replies
1.5k
views
CAGEr: Problem when running getCTSS
CAGEr
updated 4.2 years ago by
Charles Plessy
▴ 180 • written 4.4 years ago by
Sergio
• 0
0
votes
1
reply
1.2k
views
Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr
raw
Agilent
MicroarrayData
import
updated 4.2 years ago by
Gordon Smyth
53k • written 4.2 years ago by
irina.st.louis4
• 0
1
vote
12
replies
4.6k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 24 months ago by
Mary
• 0 • written 4.2 years ago by
Ming
▴ 380
1
vote
4
replies
1.5k
views
Advice to use block factor and duplicatecorrelation in RNA-seq experiment
limma
4.2 years ago
jfertaj
▴ 30
1
vote
8
replies
5.5k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
4.2 years ago
v.merino.nicolas
▴ 10
0
votes
1
reply
1.4k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
jfertaj
▴ 30
0
votes
2
replies
1.4k
views
Error in TFBSTools at SitesetList
error
TFBSTools
R
4.2 years ago
HELEN
• 0
6
votes
6
replies
2.4k
views
Batch effect from to sequencing data at differents depths
Sequencing
sequencingDeepth
BatchEffect
DESeq2
4.2 years ago
ary.lech
▴ 10
0
votes
3
replies
2.4k
views
Bioconductor 3.13 installer reports that affyQCReport is not available
Install
3.13
affyQCReport
updated 4.2 years ago by
Miguel
▴ 10 • written 4.3 years ago by
lsmatott
• 0
2
votes
1
reply
3.8k
views
Specify hg19 in using biomaRt getBM function
biomaRt
biom
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
lei.shang
• 0
0
votes
0
replies
1.3k
views
Editing KEGG pathways in R
KEGG
4.2 years ago
Jordan
• 0
2
votes
4
replies
4.8k
views
How to simply change chromosome names of a GRanges object?
genomicrang
GenomicRanges
updated 4.0 years ago by
Hervé Pagès
16k • written 4.2 years ago by
changxu.fan
▴ 20
1
vote
1
reply
2.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
n.vandis
• 0
0
votes
0
replies
3.7k
views
Circlize - Error: not enough space for cells at track index '5'.
circlize
4.2 years ago
lessismore
▴ 20
0
votes
2
replies
1.4k
views
problems opening ChAMP
ChAMP
updated 4.2 years ago by
Basti
▴ 780 • written 4.2 years ago by
AaVee
• 0
1
vote
3
replies
1.3k
views
Example from TissueEnrich documentation throws error
TissueEnrich
4.2 years ago
sarvesh.nikumbh
▴ 10
1
vote
1
reply
2.2k
views
Help understanding edgeR code for doing exactTest
exacttest
RNASeqData
edgeR
diffGeneAnalysis
updated 4.2 years ago by
Gordon Smyth
53k • written 4.2 years ago by
Julia
• 0
0
votes
0
replies
728
views
Error in infinityFlow
infinityFlow
4.2 years ago
Niv
• 0
0
votes
3
replies
1.9k
views
Problem select / ensembl package
ensembldb
4.2 years ago
yinnahm
• 0
0
votes
2
replies
2.4k
views
AnnotationDbi
AnnotationDbi
4.2 years ago
Bogdan
▴ 670
1
vote
2
replies
2.1k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
4.2 years ago
raf4
▴ 30
2
votes
4
replies
2.1k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 4.2 years ago by
Gordon Smyth
53k • written 4.3 years ago by
rebecca.lea.johnston
• 0
2
votes
1
reply
1.3k
views
preprocessReads: Can't remove more than 17 nucleotides
QuasR
preprocessReads
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
sha-ked
• 0
0
votes
1
reply
1.1k
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink
DESeq2
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
Nayrouz
• 0
0
votes
1
reply
680
views
Interaction model genes don't intersect
DESeq2
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
jd348
• 0
0
votes
0
replies
1.6k
views
Job:
Bioinformatician position at University of Texas Southwestern Medical Center
Sequencing
bioinformatics
4.2 years ago
chao.xing
• 0
3
votes
3
replies
1.1k
views
Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq
DESeq2
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
Delta._.43
▴ 20
2
votes
2
replies
2.1k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3
recountWorkflow
updated 4.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.3 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
1
reply
1.4k
views
Different read support for splice junctions using snapcount and recount3
recount3
snapcount
updated 4.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.3 years ago by
mario.keller.1988
▴ 20
3
votes
2
replies
1.6k
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
4.2 years ago
Debayan
▴ 20
0
votes
2
replies
1.9k
views
Correct workflow for analyzing differentially expressed genes and correlation analyses on TCGA data?
DESeq2
4.2 years ago
mario.keller.1988
▴ 20
4
votes
1
reply
3.2k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene
RNASeqR
DESeq2
RNAseq
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
sohail.mbio
▴ 10
1
vote
4
replies
1.4k
views
Error in designing DESeq2 time pointed experiments
LTR
DESeq2
4.2 years ago
AZ
▴ 20
0
votes
0
replies
916
views
Calculate AUC from CellTiter-Glo luminance data in R
highthroughputassays
drc
4.2 years ago
yura.grabovska
▴ 30
0
votes
2
replies
1.3k
views
results() function and finding the difference of differences
interactions
DESeq2
4.2 years ago
Nayrouz
• 0
1
vote
0
replies
1.1k
views
Job:
Faculty Position in Computer Science applied to Medical Sciences @ UCLouvain
JobPosting
4.2 years ago
Laurent Gatto
1.6k
0
votes
1
reply
818
views
pd.ragene.2.0
pd.ragene.2.0.st
updated 4.2 years ago by
James W. MacDonald
68k • written 4.2 years ago by
Belen
• 0
0
votes
8
replies
3.7k
views
TCL/TK in R
TCL/TK
4.2 years ago
Bogdan
▴ 670
1
vote
0
replies
2.2k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
4.2 years ago
makrez
▴ 10
3
votes
3
replies
2.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
4.2 years ago
enricoferrero
▴ 680
0
votes
0
replies
897
views
Y axis Data Track GVIZ
GVIZ
4.2 years ago • updated 4.1 years ago
rbenel
▴ 50
46,726 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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