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0
votes
4
replies
298
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 2 days ago
Efra
• 0
1
vote
1
reply
122
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Emma
• 0
0
votes
1
reply
100
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
0
votes
1
reply
118
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Yuqin
• 0
1
vote
7
replies
1.1k
views
enrichGOgradient color change
clusterProfiler
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 4 months ago by
inna.gur
• 0
1
vote
5
replies
331
views
Biostrings: read*StringSet() functions leave open file handles
Biostrings
20 days ago • updated 11 days ago
Gerhard Thallinger
▴ 180
4
votes
7
replies
321
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 23 hours ago by
Gordon Smyth
50k • written 12 days ago by
Amit
• 0
0
votes
2
replies
212
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
1
vote
1
reply
135
views
Perfoming clumping using ieugwasr package
LinkageDisequilibrium
genom
linka
GenomicDistributionsData
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
zoheir.alayash
▴ 10
2
votes
2
replies
160
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
13 days ago • updated 11 days ago
feather-W
• 0
0
votes
1
reply
126
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
Gerhard Thallinger
▴ 180
2
votes
2
replies
197
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 10 days ago
elesofi
• 0
2
votes
3
replies
2.1k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 12 days ago by
ATpoint
★ 4.0k • written 24 months ago by
liqidong52
▴ 20
0
votes
1
reply
128
views
problem with ClusterRepro function
WGCNA
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Antonio.Aubry
• 0
0
votes
2
replies
247
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 15 days ago by
gglatzer
• 0
0
votes
4
replies
354
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 14 days ago by
Michael Love
41k • written 14 days ago by
Jad
• 0
2
votes
2
replies
187
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
14 days ago
Sabiha
▴ 20
0
votes
7
replies
338
views
DESeq2 filtering vs edgeR filtering
DESeq2
15 days ago • updated 2 days ago
fr8712ca-s
• 0
0
votes
2
replies
174
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 14 days ago
Sam
▴ 10
0
votes
2
replies
161
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
15 days ago • updated 14 days ago
kcarey
• 0
1
vote
1
reply
166
views
i'm not getting any differentially expressed genes.
DESeq2
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Marilyn
• 0
2
votes
1
reply
191
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
hemantcnaik
• 0
0
votes
1
reply
165
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 16 days ago by
BioinfoMug
• 0
0
votes
1
reply
143
views
Exact same results in Diffbind with different normalization methods
DiffBind
16 days ago • updated 11 days ago
red_bricks
▴ 50
0
votes
0
replies
101
views
FELLA plotGraph function won't change the legend
FELLA
16 days ago
yuhang
• 0
0
votes
0
replies
99
views
medips-output
ngsReports
MEDIPS
16 days ago
subhiksha
• 0
0
votes
0
replies
96
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
16 days ago
bocsci11
• 0
0
votes
1
reply
210
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 17 days ago by
Fabricio Almeida-Silva
▴ 40 • written 8 weeks ago by
Sujeevan
• 0
0
votes
1
reply
235
views
question about data processing for syntenet
syntenet
updated 17 days ago by
Fabricio Almeida-Silva
▴ 40 • written 11 weeks ago by
Sujeevan
• 0
0
votes
2
replies
264
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
28 days ago • updated 16 days ago
shepherl
3.8k
0
votes
4
replies
214
views
Error in classify_gene_pairs
syntenet
doubletrouble
17 days ago • updated 16 days ago
hfyuan2016
• 0
0
votes
1
reply
106
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
maltethodberg
▴ 170
0
votes
0
replies
86
views
The graphical interface of FELLA doesn't work
FELLA
17 days ago
yuhang
• 0
0
votes
0
replies
93
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
17 days ago
jean-christophe.helbling
• 0
1
vote
1
reply
160
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.0k • written 18 days ago by
synat.keam
• 0
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
0
votes
2
replies
272
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 days ago • updated 19 days ago
Viktor Thiel
• 0
0
votes
0
replies
109
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
20 days ago
Henry
• 0
0
votes
1
reply
152
views
Rcpp compilation error
Release
Rcpp
updated 20 days ago by
ATpoint
★ 4.0k • written 20 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
110
views
Rain error: invalid annotation of time points
rain
21 days ago
mpuli011
• 0
0
votes
0
replies
103
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
21 days ago
Felix
• 0
0
votes
1
reply
136
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
185
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 days ago
thomas
• 0
1
vote
1
reply
142
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
ronin
• 0
0
votes
8
replies
293
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago
michelafrancesconi8
• 0
0
votes
1
reply
150
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Sneha
• 0
0
votes
0
replies
109
views
News:
Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
21 days ago
cv.jam.zhxf17875
• 0
0
votes
6
replies
324
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
21 days ago • updated 2 days ago
Lily Cheang
• 0
3
votes
8
replies
416
views
Constrast for Time Course Experiments using Limma
limma
23 days ago • updated 21 days ago
dl17032000
• 0
1
vote
4
replies
233
views
DESeq2 Replicates
DESeq2
RNASeq
21 days ago
kcarey
• 0
1,000 results • Page
2 of 20
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Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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