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7
replies
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U-shape of p-value histograms is removed by filtering for genes that have >5 counts in >10% of samples before applying DESeq2 analysis
deseq2
p-value distribution
U-shaped
pre-filter low counts
7.0 years ago
stu111538
• 0
0
votes
4
replies
3.5k
views
biomaRt: Unexpected format to the list of available marts.
software error
biomaRt
7.0 years ago
frank007
• 0
0
votes
1
reply
1.3k
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
lalchungnungabt17
• 0
4
votes
4
replies
1.9k
views
Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
limma
stageR
decideTests
updated 7.0 years ago by
Koen Van den Berge
▴ 180 • written 7.0 years ago by
maltethodberg
▴ 180
2
votes
5
replies
2.2k
views
Error loading Gviz package object path is not exported by namespace:Rsamtools
gviz
rsamtools
updated 7.0 years ago by
solutionsweb770
• 0 • written 7.0 years ago by
frequena.sanchez
• 0
3
votes
7
replies
1.9k
views
Using varianceStabilizingTransformation (VST) with no replications?
deseq2
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Sarah_piggy
▴ 10
3
votes
9
replies
3.4k
views
Differential transcript expression (DTE) analysis
rnaseqDTU
dtu
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
rbenel
▴ 50
0
votes
0
replies
974
views
TPP error message " The names of the data objects in 'data' differ from the names given in the Experiment column of 'configTable'."
software error
TPP
updated 7.0 years ago by
shepherl
4.3k • written 7.0 years ago by
kkim369
• 0
0
votes
3
replies
2.1k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
Bogdan
▴ 670
0
votes
4
replies
1.7k
views
MSnset combine error message
MSnbase
7.0 years ago
kamal.fartiyal84
▴ 10
2
votes
2
replies
1.6k
views
rnaseqDTU DTU workflow - pots-hoc Filter
DTU
DRIMSeq
rnaseqDTU
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
fiona.dick91
▴ 60
0
votes
5
replies
5.0k
views
Errors installing RforProteomics and MSnbase packages
RforProteomics
MSnbase
updated 7.0 years ago by
Laurent Gatto
1.6k • written 7.0 years ago by
fgol
▴ 10
1
vote
2
replies
1.8k
views
How to remove samples from EDAseq SeqExpressionSeq
EDAseq
updated 7.0 years ago by
davide risso
▴ 980 • written 7.0 years ago by
Jon Bråte
▴ 270
0
votes
3
replies
2.1k
views
extracting scaffoldnames from HiC contact matrix
hic
updated 7.0 years ago by
bioparticles.melly
• 0 • written 7.0 years ago by
m.t.lorenc
• 0
3
votes
7
replies
1.8k
views
Limma analysis, controlling for Donors.
limma
r
microarray
updated 7.0 years ago by
Gordon Smyth
53k • written 7.0 years ago by
reubenmcgregor88
• 0
1
vote
0
replies
1.0k
views
Job:
NGS Technical Applications Scientist
#sequencing
#NGS
#FAS
#fieldsupport
Job
7.0 years ago
paul
▴ 10
1
vote
1
reply
1.7k
views
DESeq2 - lfcShrink with list contrast on grouped variable
deseq2
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
gcagle1
• 0
3
votes
3
replies
1.8k
views
limma for getting DEGs from my own input matrix
limma
updated 7.0 years ago by
Aaron Lun
★ 29k • written 7.0 years ago by
shuvadeep.maity
• 0
2
votes
1
reply
1.1k
views
Go back to GRanges used as RaggedExperiment input
RaggedExperiment
updated 7.0 years ago by
Marcel Ramos
700 • written 7.0 years ago by
Vinicius Henrique da Silva
▴ 40
2
votes
2
replies
1.7k
views
What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
deseq2
PCAplot
Visualization
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Mithil Gaikwad
• 0
0
votes
7
replies
1.8k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2
design
timeseries
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
indrik.wijaya
▴ 20
4
votes
3
replies
1.7k
views
RSubread in cygwin
subread
7.0 years ago
Diana
▴ 10
1
vote
1
reply
1.8k
views
read.FCS memory limit? - $PnRNAis larger than R's numeric limit
flowCore
read.FCS
memory_limit
7.0 years ago
lloyd.izard
▴ 80
0
votes
1
reply
1.6k
views
consulting about the FELLA package
software error
FELLA
updated 7.0 years ago by
sergi.picart
▴ 20 • written 7.0 years ago by
jnzd_hemaozhang
• 0
1
vote
6
replies
2.3k
views
edgeR for time series
edgeR
updated 7.0 years ago by
Gordon Smyth
53k • written 7.0 years ago by
sharvari gujja
▴ 40
0
votes
3
replies
2.2k
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq
TissueEnrich
tissue-specific expression
differential expression
updated 7.0 years ago by
Ashish Jain
▴ 10 • written 7.0 years ago by
andrew.oler
• 0
0
votes
0
replies
856
views
WEBBIOC
updated 7.0 years ago by
Bioconductor Community
0 • written 19.4 years ago by
Verma, Seema
▴ 10
2
votes
10
replies
4.4k
views
ChIPpeakAnno, MACS format annotation
bioconductor
ChIPpeakAnno
updated 7.0 years ago by
Julie Zhu
★ 4.3k • written 8.8 years ago by
Khademul Islam
▴ 30
3
votes
6
replies
1.6k
views
Handling multiple knockout experiments with DESeq2
deseq2
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
cmfield
• 0
0
votes
0
replies
1.4k
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe
affy
probe
affy
updated 7.0 years ago by
Bioconductor Community
0 • written 21.9 years ago by
Matthew Hannah
▴ 940
0
votes
1
reply
893
views
signeR errors when assessing for variant signatures
software error
updated 7.0 years ago by
renan.valieris
▴ 10 • written 7.0 years ago by
Dan
• 0
0
votes
0
replies
800
views
R ArrayExpress probleme
R
7.0 years ago
hafidimustapha
• 0
2
votes
4
replies
3.8k
views
Problem installing GenomicRanges package
software error
7.0 years ago
aigofaith
▴ 10
0
votes
1
reply
1.7k
views
Help on contrast matrix Limma
updated 7.0 years ago by
Bioconductor Community
0 • written 16.3 years ago by
Gordon Smyth
53k
0
votes
0
replies
994
views
kegg enrichment using clusterProfiler could not provide gene name
annotation
7.0 years ago
huangzhiguang2016
• 0
0
votes
1
reply
2.1k
views
gcrma background correction-saving output
cdf
affy
gcrma
matchprobes
affyio
cdf
affy
gcrma
matchprobes
affyio
updated 7.0 years ago by
Bioconductor Community
0 • written 19.1 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.4k
views
VCF files incompatible with signeR
software error
signeR
7.0 years ago
Dan
• 0
0
votes
1
reply
878
views
error while runing Bioconductro install script
updated 7.0 years ago by
Bioconductor Community
0 • written 22.7 years ago by
Berislav Bosnjak
▴ 10
1
vote
4
replies
2.5k
views
Error : Salmon tximport to DESeq2
deseq2
tximport
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
saddamhusain77
• 0
0
votes
0
replies
975
views
error in reading CEL file
updated 7.0 years ago by
Bioconductor Community
0 • written 21.4 years ago by
Lana Schaffer
▴ 80
0
votes
2
replies
1.4k
views
LIMMA: how to assign file name
limma
ASSIGN
limma
ASSIGN
updated 7.0 years ago by
Bioconductor Community
0 • written 20.7 years ago by
Guoneng Zhong
▴ 180
0
votes
1
reply
1.8k
views
flowDensity loop on flowSet
flowdensity
flowcore
for loop
updated 7.0 years ago by
Bioconductor Community
0 • written 7.2 years ago by
beshea.jj
• 0
0
votes
1
reply
1.3k
views
Add interaction term between variables to DEXSeq design
DEXSeq
interaction
7.0 years ago
zhenzuo2
• 0
0
votes
0
replies
1.4k
views
Job:
Postdoc in Bioinformatics (UCSF Benioff Children's Hospital Oakland)
Bioinformatics
RNA-seq
Postdoc
Genomics
Statistical model
Job
7.0 years ago
djawaheer
• 0
0
votes
5
replies
2.6k
views
Error:no method for coercing this S4 class to a vector
annotation
genomation
updated 7.0 years ago by
altuna akalin
▴ 20 • written 7.0 years ago by
janani.sundaresan
• 0
0
votes
3
replies
2.1k
views
tri.counts.method parameter in deconstructSigs
deconstructsigs
updated 7.0 years ago by
Bioconductor Community
0 • written 9.0 years ago by
Jane Merlevede
▴ 90
1
vote
0
replies
1.3k
views
Job:
Staff researcher position in biostatistics / data science consulting at EMBL
EMBL
Job
7.0 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
1.3k
views
error importing bam file for MEDIPS analysis
MEDIPS
bamfile
updated 7.0 years ago by
Bioconductor Community
0 • written 7.2 years ago by
oussama.badad
• 0
0
votes
3
replies
2.4k
views
Algorithm for between and within microarray normalisation (for meta-analysis).
microarray
meta-analysis
gene expression
updated 7.0 years ago by
Bioconductor Community
0 • written 9.5 years ago by
StephK
▴ 70
6
votes
14
replies
3.8k
views
Paired analysis setup using edgeR - follow up question
edger
7.0 years ago
candida.vaz
▴ 50
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