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0
votes
3
replies
3.2k
views
Annotation in ExpressionSet object
ExpressionSet
globaltest
9.6 years ago
NS
▴ 60
1
vote
3
replies
1.7k
views
VennDiagram from two TestResults matrices
limma
venn diagram
updated 9.6 years ago by
Gordon Smyth
53k • written 9.6 years ago by
shania90.lk
▴ 10
0
votes
0
replies
1.5k
views
plotting normalized RPM coverage for plus and minus strands in gviz
gviz
rsamtools
9.6 years ago
amias
▴ 10
1
vote
5
replies
2.4k
views
Error using Rsubread align: caugh segfault invalid permissions
rsubread
align
segfault
updated 9.6 years ago by
Wei Shi
★ 3.6k • written 9.6 years ago by
gerard_llimos
▴ 10
9
votes
6
replies
4.5k
views
about paired-samples in edgeR
edger
9.6 years ago
Bogdan
▴ 670
0
votes
1
reply
1.2k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
wliao
• 0
1
vote
4
replies
2.6k
views
DESeq2 "results" Error in .classEnv(classDef)
deseq2
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
p2016k
• 0
2
votes
25
replies
8.4k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
9.7 years ago • updated 9.6 years ago
sami.pietila
• 0
2
votes
6
replies
3.9k
views
Clustering and bootstrapping of RNASeq samples
clustering
pvclust
vsd
edgeR
rnaseq
written 9.6 years ago by
Jane Merlevede
▴ 90
0
votes
0
replies
2.0k
views
methyAnalysis error with example data
methyanalysis
9.6 years ago
Tom
▴ 10
1
vote
4
replies
1.8k
views
Error using countBam (Rsamtools package)
rsamtools
countbam
9.6 years ago
t.kuilman
▴ 170
0
votes
0
replies
1.0k
views
How to calculate risk of relapse based on subtypes and proliferation (ROR-P) PAM50 sub-typing?
RORP
PAM50
9.6 years ago
g_draculla
▴ 10
0
votes
3
replies
2.0k
views
Trouble with Custom PC Plot
deseq2
plotPCA
PCA
rna-seq
9.6 years ago
newsomew13
• 0
0
votes
1
reply
953
views
question for SVA package
getting error in gsva function
updated 9.6 years ago by
Jeff Leek
▴ 650 • written 9.6 years ago by
js2182
• 0
5
votes
4
replies
2.1k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 9.6 years ago by
Hervé Pagès
16k • written 9.6 years ago by
endrebak85
▴ 40
1
vote
1
reply
2.4k
views
Null model in SVA for patient paired test comparing tumor vs normal
sva
paired samples
rnaseq
updated 9.6 years ago by
Jeff Leek
▴ 650 • written 9.6 years ago by
gumilton
• 0
0
votes
6
replies
3.1k
views
EBImage readImage hangs when reading tif file with multiple frames.
software error
ebimage
updated 9.6 years ago by
Andrzej Oleś
▴ 750 • written 9.6 years ago by
krassk
• 0
0
votes
1
reply
1.2k
views
[VariantAnnotation] Unable to set a genotype with geno()
variantannotation
updated 9.6 years ago by
shepherl
4.2k • written 9.6 years ago by
delphine.charif
• 0
1
vote
6
replies
1.8k
views
Are these contrasts correct for use in DESeq2?
deseq2
contrast
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
Jane Merlevede
▴ 90
6
votes
4
replies
2.2k
views
Clarification on DESeq2 normalizationFactors(), estimateDispersions() and varianceStabilizingTransformation()
deseq2
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
enricoferrero
▴ 680
5
votes
7
replies
2.6k
views
Gviz: How to plot UTRs with GRanges object?
gviz
updated 9.6 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.6 years ago by
stianlagstad
▴ 90
2
votes
5
replies
2.8k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz
bam
pacbio
updated 9.6 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.6 years ago by
thackl
• 0
0
votes
0
replies
1.3k
views
[EBSeq] Normalization and DE genes detection
ebseq
normalization
differential gene expression
9.6 years ago
jean.keller
▴ 10
0
votes
6
replies
5.5k
views
Nonexistent include directory
software error
r package problem
updated 9.6 years ago by
Martin Morgan
25k • written 9.6 years ago by
kkp7700
• 0
4
votes
5
replies
7.0k
views
Hisat2 vs featureCounts summary statistics
featurecounts
hisat2
rna-seq
mapping
updated 9.6 years ago by
Wei Shi
★ 3.6k • written 9.7 years ago by
Koen Van den Berge
▴ 180
5
votes
2
replies
13k
views
lowess vs. loess
Microarray
Normalization
updated 9.6 years ago by
Gordon Smyth
53k • written 22.4 years ago by
nataraja@mit.edu
▴ 30
1
vote
1
reply
951
views
hom.Hs.inp_dbschema of the Inparanoid annotation package not working properly
software error
annotationdbi
updated 9.6 years ago by
Hervé Pagès
16k • written 9.6 years ago by
Burak Kutlu
• 0
2
votes
2
replies
1.6k
views
taking intersection between 6 networks by graph.intersect
igraph
software error
adjacency matrix
updated 9.6 years ago by
Paul Shannon
▴ 470 • written 9.6 years ago by
Angel
▴ 40
3
votes
1
reply
1.5k
views
parsing flowFrame@description in flowCore
FCS file
flowcore
@description
updated 9.6 years ago by
Jiang, Mike
★ 1.3k • written 9.6 years ago by
Robert Baer
▴ 70
1
vote
3
replies
2.1k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma
microarray
linear model
statistical modeling
model.matrix
9.6 years ago
christopher.clarskon15
▴ 20
0
votes
1
reply
1.7k
views
ggbio OrganismDb autoplot - reduce vs identity
ggbio
autoplot
updated 9.6 years ago by
James W. MacDonald
68k • written 9.6 years ago by
Lescai, Francesco
▴ 380
0
votes
0
replies
1.5k
views
AnnotationData Packages version and pipeline management
docker
annotation
pipeline
9.6 years ago
Elena Grassi
▴ 10
3
votes
10
replies
2.8k
views
Combining data from multiple illumina microarray experiments
normalization
limma
updated 9.6 years ago by
Gordon Smyth
53k • written 9.6 years ago by
chris86
▴ 420
0
votes
3
replies
1.7k
views
DiffBind dba.count() seqfault
diffbind
dba.count
9.6 years ago
em540
• 0
0
votes
1
reply
1.0k
views
DESeq erroneously normalizing all values to mean of one specific variable - what's wrong?
deseq2
normalization
fitType
parametric
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
stwestreich
• 0
4
votes
5
replies
1.8k
views
XStringSet operations discard names - how to address?
biostrings
updated 9.6 years ago by
Hervé Pagès
16k • written 9.6 years ago by
nicholasbauer
• 0
2
votes
6
replies
7.1k
views
PCA in DESeq2 - Can I get the genes contributing most to each component?
deseq2
pca
9.6 years ago
Emily
▴ 10
2
votes
2
replies
2.7k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2
rnaseq
contrast
multiple comparisons
fdrtool
9.6 years ago
sebastiano.curreli
• 0
5
votes
12
replies
6.3k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2
edgeR
differential gene expression
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
Jane Merlevede
▴ 90
4
votes
2
replies
5.0k
views
DESeq2 color coding
DESeq2
color
R package
updated 9.6 years ago by
Mike Smith
★ 6.6k • written 9.6 years ago by
ChIP-Tease
• 0
6
votes
11
replies
2.9k
views
microarray data analsis with limma?
limma
genepix
microarray
agilent microarrays
9.6 years ago
Mehmet Ilyas Cosacak
• 0
3
votes
3
replies
2.4k
views
pairwiseAlignments coordinate mapping?
biostrings
pairwisealignment
updated 8 months ago by
rohitsatyam102
▴ 20 • written 9.6 years ago by
Steve Lianoglou
★ 13k
2
votes
1
reply
2.3k
views
GEOquery::getGEO warning: not all columns named in 'colClasses' exist
GEOquery
updated 9.6 years ago by
Sean Davis
21k • written 9.6 years ago by
alexvpickering
▴ 110
4
votes
5
replies
1.5k
views
DESeq2 how to define my conditions when I want the results comparing a subset of samples
deseq2
rnaseq
updated 9.6 years ago by
Ryan C. Thompson
★ 7.9k • written 9.6 years ago by
ldetorrente
▴ 10
0
votes
1
reply
1.2k
views
offTargetAnalysis result interpretation
crisprseek
updated 9.6 years ago by
Julie Zhu
★ 4.3k • written 9.6 years ago by
krababah
• 0
0
votes
1
reply
2.3k
views
Adjusting microarray data using ComBat and SVA
sva
sva
updated 9.6 years ago by
cathytian2011
• 0 • written 13.0 years ago by
Mirza, Nasir
▴ 40
1
vote
1
reply
2.4k
views
DESeq2 independent filtering fails to filter low counts
deseq2
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
nschaum
• 0
1
vote
1
reply
1.0k
views
DESeq2 feature request: parallelised refitWithoutOutliers()
DESeq2
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
aatsmith
• 0
0
votes
3
replies
4.7k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo
biomart
gene ontology
goexpress
pathway analysis
updated 9.6 years ago by
kevin.rue
▴ 350 • written 9.6 years ago by
Darya Vanichkina
▴ 130
6
votes
10
replies
3.3k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 9.6 years ago by
Johannes Rainer
★ 2.1k • written 9.6 years ago by
stianlagstad
▴ 90
46,706 results • Page
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Just like attending workshops helps you improve skills in a field, playing 8 Ball Pool helps sharpen your strategy and precision. You can d…
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• 0
Thanks for sharing this update. Clear migration timelines and documentation are essential for learners and researchers alike. In healthcare…
Comment: ATACseq rudimentary questions
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4747
• 0
Thank you so much for being detailed, all makes sense now
Answer: How to do differential expresion across time serise with edgeR?
by
Gordon Smyth
53k
You actually haven't done any DE analysis at all, you've just selected for genes with either zero or large D0 counts. Another issue is tha…
Answer: ATACseq rudimentary questions
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★ 4.0k
For differential analysis tools like DiffTF and TOBIAS, the standard and statistically sound approach is to create **one large consensus pe…
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