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0
votes
0
replies
27
views
Deseq2 Time series - 2 treatments 1 control 6 Time Points
timecourse
DESeq2
20 hours ago
Maria
• 0
0
votes
0
replies
24
views
what is the format of DMPfinder in minfi package
minfi
20 hours ago
Fateme
• 0
4
votes
3
replies
5.3k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 1 day ago by
wahaha
• 0 • written 4.6 years ago by
anton.kratz
▴ 60
2
votes
5
replies
190
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
26 days ago • updated 1 day ago
Nicole
• 0
1
vote
3
replies
77
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R
edgeR
updated 1 day ago by
Gordon Smyth
45k • written 1 day ago by
Mohamed
• 0
0
votes
2
replies
54
views
Italicise
EnhancedVolcano
1 day ago • updated 20 hours ago
Pau
• 0
0
votes
1
reply
33
views
Discrepancy between plot colours during exomeCopy tutorial
exomeCopy
updated 1 day ago by
Michael Love
37k • written 1 day ago by
joel.wallenius
• 0
0
votes
1
reply
57
views
Help with constructing design matrix for edgeR/limma
limma
design.matrix
model.matrix
edgeR
updated 1 day ago by
Gordon Smyth
45k • written 2 days ago by
adrianna_07
• 0
0
votes
1
reply
83
views
Trouble with detecting AS events using ASpediaFI
ASpediaFI
updated 2 days ago by
rbqlsrbqls56
• 0 • written 17 days ago by
rezashiralmohammad
• 0
2
votes
2
replies
100
views
edgeR : results from goana and kegga functions show opposite sig. p-value
edgeR
2 days ago
sharvari gujja
▴ 30
3
votes
6
replies
168
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
3 days ago
JK Kim
• 0
1
vote
1
reply
53
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 3 days ago by
James W. MacDonald
60k • written 3 days ago by
ramonfallon
• 0
0
votes
6
replies
137
views
help please!
TargetScoreData
updated 2 days ago by
shepherl
3.1k • written 3 days ago by
1051444231
• 0
2
votes
2
replies
1.3k
views
Feature request: syntax for dropping unused seqlevels in GRanges objects
granges
seqlevels
feature request
updated 3 days ago by
story.benjamin
▴ 10 • written 5.0 years ago by
Charles Plessy
▴ 170
0
votes
1
reply
50
views
unable to install RBGL
#RBGL
updated 3 days ago by
James W. MacDonald
60k • written 4 days ago by
baldwinh555
• 0
0
votes
1
reply
65
views
NMF installation with current R version
NMF
Biobase
updated 3 days ago by
shepherl
3.1k • written 17 days ago by
Abhishek
• 0
0
votes
0
replies
48
views
Job:
Bioconductor Community Manager
Community
Teaching
Bioconductor
5 days ago • updated 3 days ago
Matthew Ritchie
▴ 1000
0
votes
1
reply
78
views
Creating DESeq object and choosing a contrast
DESeq2
updated 3 days ago by
Michael Love
37k • written 4 days ago by
Dev Raj
• 0
0
votes
1
reply
45
views
exomeCopy warning and error
exomeCopy
updated 3 days ago by
Michael Love
37k • written 3 days ago by
ef.kafantari
• 0
0
votes
2
replies
81
views
Fail to run RupRadar
dupRadar
4 days ago • updated 3 days ago
Qingwei
• 0
0
votes
2
replies
96
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt
AnnotationForge
4 days ago • updated 3 days ago
Lan Anh
• 0
0
votes
0
replies
65
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
4 days ago • updated 2 days ago
NIK
• 0
0
votes
2
replies
107
views
RPX PXDataset error
PRIDE
rpx
PXDataset
updated 4 days ago by
Laurent Gatto
1.5k • written 11 days ago by
gianluigi.caltabiano
• 0
0
votes
0
replies
41
views
Not obtaining significant Gene Ontology Biological Process hits
clusterProfiler
4 days ago
Jordan
• 0
0
votes
2
replies
77
views
Package name already exists due to previous issue
Bioconductor
updated 4 days ago by
shepherl
3.1k • written 5 days ago by
Daan
• 0
0
votes
4
replies
133
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3 days ago by
Hervé Pagès
15k • written 6 days ago by
rsnorman
• 0
2
votes
7
replies
184
views
CPM after RUVseq
RUVSeq
CPM
Normalization
7 days ago • updated 3 days ago
Jess
• 0
3
votes
3
replies
93
views
Merging two plated in R
dese
DESeq2
updated 4 days ago by
James W. MacDonald
60k • written 4 days ago by
lmrogers34
• 0
0
votes
2
replies
266
views
layout has more positions than samples but omixerRand doesn't randomize the samples
Omixer
13 months ago • updated 4 days ago
Lluís Revilla Sancho
▴ 660
1
vote
4
replies
132
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 4 days ago by
Kevin Blighe
3.5k • written 5 days ago by
beslinail
• 0
1
vote
1
reply
73
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma
lmfit
R
DifferentialExpression
updated 4 days ago by
ATpoint
★ 1.2k • written 4 days ago by
Dimitris
• 0
0
votes
1
reply
198
views
Can GSVA be applied in several sample type and each type only have two replicates ?
GSVA
updated 4 days ago by
Robert Castelo
★ 2.9k • written 9 months ago by
Guandong Shang
▴ 20
3
votes
3
replies
128
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 4 days ago by
Gordon Smyth
45k • written 5 days ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
49
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression
DiffBind
5 days ago • updated 4 days ago
Luca
• 0
0
votes
6
replies
165
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
5 days ago • updated 4 days ago
nabiyogesh
▴ 10
2
votes
6
replies
204
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq
DESeq2
7 days ago • updated 5 days ago
andrebolerbarros
▴ 10
0
votes
1
reply
73
views
scRNASeq reference at a transcript level
EWCE
scRNAseq
updated 5 days ago by
Basti
▴ 300 • written 5 days ago by
marc.tormo
• 0
2
votes
2
replies
73
views
How to run GSVA with partially NA genes
GSVA
6 days ago • updated 5 days ago
blakebowen
• 0
0
votes
2
replies
190
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 24 days ago by
curiousmind007
• 0
0
votes
2
replies
105
views
Using limma to read Illumina HT-12 v4 data
limma
updated 7 days ago by
Gordon Smyth
45k • written 7 days ago by
orbitofrontal
• 0
0
votes
4
replies
152
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 6 days ago by
ATpoint
★ 1.2k • written 9 days ago by
Bogdan
▴ 640
0
votes
2
replies
83
views
R: problem with running time-series analysis software: Mfuzz
time-series
mfuzz
replace=FALSE
8 days ago • updated 7 days ago
soda
▴ 80
1
vote
4
replies
150
views
ashr vs apeglm for interaction data
lfcShrink
DESeq2
10 days ago • updated 5 days ago
Ali Barry
▴ 30
2
votes
4
replies
127
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219
oligo
AffymetrixChip
8 days ago
Yang Shi
• 0
1
vote
5
replies
159
views
UniprotKB AC/ID to Entrez ID Conversion
ID
Uniprot
EntrezID
8 days ago • updated 5 days ago
tom.kloter
• 0
2
votes
2
replies
89
views
how to make a group to apply the data to CAMERA
CAMERA
8 days ago • updated 7 days ago
Akira
• 0
4
votes
10
replies
240
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
10 days ago • updated 8 days ago
Yang Shi
• 0
4
votes
6
replies
209
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
10 days ago • updated 5 days ago
mohammedtoufiq91
▴ 10
1
vote
4
replies
258
views
different results in DESeq2 when comparing groups in two ways
DESeq2
10 days ago • updated 9 days ago
zohreh.fazelan
• 0
0
votes
1
reply
107
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 8 days ago by
ATpoint
★ 1.2k • written 9 days ago by
johnmcma
▴ 10
42,570 results • Page
1 of 852
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Replies
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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