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0
votes
0
replies
11
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
5 hours ago
kyj2226
• 0
2
votes
4
replies
188
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 6 hours ago by
Gordon Smyth
49k • written 1 day ago by
kyj2226
• 0
0
votes
3
replies
116
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip
limma
goana
updated 17 hours ago by
SamGG
▴ 320 • written 1 day ago by
samagbeyimodupe
• 0
0
votes
3
replies
2.5k
views
Problems with FLOWAI
flowAI
updated 2 days ago by
Alexander
• 0 • written 2.6 years ago by
msoares
• 0
1
vote
1
reply
95
views
Asses fit of variance prior
limma
updated 2 days ago by
Gordon Smyth
49k • written 2 days ago by
Frederik Ziebell
▴ 20
0
votes
1
reply
100
views
Interaction terms in DESeq2
RNASeqData
RnaSeqSampleSize
DESeq2
updated 2 days ago by
James W. MacDonald
64k • written 2 days ago by
Mimi
• 0
0
votes
0
replies
32
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
updated 2 days ago by
Michael Love
41k • written 2 days ago by
aehall26
• 0
0
votes
2
replies
87
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
2 days ago
Bine
▴ 20
3
votes
12
replies
1.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
Bioconductor
devel
Devel
5 months ago • updated 3 days ago
shepherl
3.6k
0
votes
0
replies
35
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
3 days ago
Sam
▴ 10
0
votes
2
replies
117
views
WGCNA documentation not available
WGCNA
updated 3 days ago by
ATpoint
★ 3.6k • written 4 days ago by
ramonmassoni
▴ 10
3
votes
2
replies
152
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 3 days ago by
Gordon Smyth
49k • written 5 days ago by
annikagable
• 0
0
votes
1
reply
80
views
biomaRt_getBM_Failed to collect lazy table
getBM
biomaRt
updated 4 days ago by
James W. MacDonald
64k • written 5 days ago by
ai.yaku
• 0
1
vote
2
replies
105
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
4 days ago
ruba-mahmoud
• 0
0
votes
1
reply
83
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 4 days ago by
ATpoint
★ 3.6k • written 4 days ago by
Miquel
• 0
0
votes
1
reply
526
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 days ago by
janetdelvalle056
• 0 • written 12 months ago by
pharamac
• 0
0
votes
3
replies
134
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
written 5 days ago by
Sitapriya
• 0
0
votes
5
replies
165
views
rDGIdb package inconsistency with web interface
rDGIdb
updated 2 days ago by
James W. MacDonald
64k • written 5 days ago by
christopherjamessteel1990
• 0
0
votes
2
replies
104
views
DESeq2 : stat or lfcshrink for GSEA analysis
lfcshrink
GSEABenchmarkeR
DESeq2
updated 2 days ago by
ATpoint
★ 3.6k • written 5 days ago by
delphine.rossille
• 0
0
votes
0
replies
48
views
autonomics: example("read_somascan", package = "autonomics") fails, but not on Bioc check servers
autonomics
5 days ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
29
views
Catalyst::cluster function does NOT produce the same results when setting seed
visua
Visualization
CATALYST
5 days ago
elefth.pavlos
▴ 40
0
votes
1
reply
737
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 5 days ago by
Vanatta
• 0 • written 2.0 years ago by
mairah.khan
• 0
1
vote
3
replies
163
views
SingleR annotation of several slots/patients
SingleR
5 days ago
Bine
▴ 20
0
votes
1
reply
78
views
How to read fcs3.2 files
flowCore
updated 5 days ago by
James W. MacDonald
64k • written 6 days ago by
Gabriel
• 0
0
votes
2
replies
106
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 6 days ago by
Stephanie M. Gogarten
▴ 870 • written 7 days ago by
Mindy wang
• 0
0
votes
2
replies
85
views
Java error while running HiCDC overview code
JuicerTools
HiC
HiCDCPlus
Java
Juicer
written 6 days ago by
IsMM
• 0
0
votes
2
replies
157
views
NCBI protein conversion to CDNA and NCBI gene (in R)
convert
updated 6 days ago by
James W. MacDonald
64k • written 8 days ago by
R_Page
• 0
0
votes
3
replies
189
views
How does Deseq2 deal with the row with zero when calculating size factors
DESeq2
written 6 days ago by
jiakang
• 0
1
vote
2
replies
169
views
RNASeq time course analysis, missing time points for control
RNASeqData
RnaSeqSampleSize
RNASeq
RNASeqPower
7 days ago • updated 6 days ago
drewhaydensteele
• 0
0
votes
8
replies
263
views
GOslim missing GO term
GO.db
GOslim
9 days ago
amanda
• 0
0
votes
3
replies
116
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 6 days ago by
Robert Castelo
★ 3.0k • written 9 days ago by
bd2000
• 0
8
votes
6
replies
406
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
updated 3 days ago by
Tim Peters
▴ 160 • written 10 days ago by
Daniel E. Weeks
▴ 30
1
vote
2
replies
114
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 9 days ago by
Gordon Smyth
49k • written 10 days ago by
Jurgen
• 0
3
votes
2
replies
185
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 10 days ago by
Gordon Smyth
49k • written 10 days ago by
annikagable
• 0
2
votes
3
replies
222
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
11 days ago • updated 8 days ago
R_Page
• 0
1
vote
1
reply
115
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 10 days ago by
ATpoint
★ 3.6k • written 11 days ago by
kaurprab
• 0
0
votes
7
replies
251
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 10 days ago by
Basti
▴ 740 • written 10 days ago by
486342583
• 0
0
votes
3
replies
215
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler
OrganismDb
updated 10 days ago by
Guido Hooiveld
★ 3.8k • written 10 days ago by
Aastha Kapoor
• 0
0
votes
1
reply
63
views
analysis of overexpressed proteins in metaproteomes
Proteomics
ProteoMM
ProteomicsWorkflow
Proteome
written 11 days ago by
ary.lech
▴ 10
0
votes
0
replies
48
views
Rgraphviz - exported (toFile) dot file loses colour and label information
Rgraphviz
11 days ago
sterlinggunn01
• 0
0
votes
3
replies
154
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 4 days ago by
Ou, Jianhong
★ 1.3k • written 11 days ago by
jfmay
• 0
0
votes
1
reply
136
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
updated 11 days ago by
James W. MacDonald
64k • written 11 days ago by
Levi
• 0
0
votes
0
replies
69
views
multipollutant models
statistics
Regression
r
limma
11 days ago
Jitendra
▴ 10
1
vote
1
reply
110
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 11 days ago by
Robert Castelo
★ 3.0k • written 12 days ago by
snijesh
▴ 20
1
vote
0
replies
53
views
Attempting to import SBML file using R
SBMLR
sbml
rsbm
rsbml
updated 6 days ago by
Michael Love
41k • written 12 days ago by
isasg
▴ 10
0
votes
1
reply
88
views
SingleR Book Not Found
SingleR
updated 12 days ago by
Peter Hickey
▴ 650 • written 12 days ago by
jgattiker
• 0
3
votes
2
replies
261
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 12 days ago by
James W. MacDonald
64k • written 12 days ago by
mckinlee.salazar
• 0
0
votes
3
replies
141
views
bam or VCF files from GSE75010
splots
CopyNumberVariationData
written 12 days ago by
ahonya
• 0
0
votes
3
replies
196
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
18 days ago • updated 10 days ago
Karthik
• 0
0
votes
5
replies
218
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 11 days ago by
James W. MacDonald
64k • written 12 days ago by
nhaus
• 0
45,036 results • Page
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Replies
Comment: Can the limma package be applied to Log2 RUV-normalized data?
by
Gordon Smyth
49k
515 samples is certainly large enough.
Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
• 0
Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim
Comment: Agilent Microarray Gene Oncology analysis gone wrong
by
SamGG
▴ 320
Gordon said to let coef to its default value: topTable(fit, n=20)
Comment: Can the limma package be applied to Log2 RUV-normalized data?
by
Shaimaa Gamal
• 0
Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…
Comment: Agilent Microarray Gene Oncology analysis gone wrong
by
samagbeyimodupe
• 0
Thank you for the quick response. i ran the codes again and removed all the other arguments for eBayes except for fit. I ran the line of co…
Votes
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
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