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Views
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2
votes
2
replies
144
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 8 days ago
Henry
▴ 10
2
votes
5
replies
1000
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 19 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
1
reply
59
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
1
vote
2
replies
197
views
MethylKit read issue
methylKit
updated 19 days ago by
James W. MacDonald
65k • written 24 days ago by
CHEN
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 7 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
1
vote
6
replies
454
views
GSVA on separate healthy and disease datasets
GSVA
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
Lucy
▴ 60
1
vote
2
replies
179
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago
Le
• 0
1
vote
3
replies
227
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
Shaimaa Gamal
• 0
1
vote
10
replies
403
views
Obtaining pheno data from CEL files
GEO
affy
22 days ago • updated 15 days ago
Kurtis
• 0
1
vote
3
replies
809
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 16 hours ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 19 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 28 days ago
Chanderkant Chaudhary
• 0
1
vote
3
replies
251
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 27 days ago by
mercedeh.movassagh
▴ 10 • written 5 weeks ago by
María
• 0
1
vote
3
replies
320
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 9 days ago by
Gordon Smyth
50k • written 14 days ago by
Simran
• 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 days ago • updated 6 days ago
Sherin
• 0
1
vote
13
replies
236
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 5 hours ago
fernanda.backsouza
▴ 10
1
vote
4
replies
127
views
minfi::read.metharray.exp
minfiData
minfi
updated 18 hours ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
1
vote
4
replies
140
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 2 days ago by
James W. MacDonald
65k • written 6 days ago by
Mirella Aurora
• 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
Hong Thu
• 0
1
vote
0
replies
31
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
15 hours ago
ATpoint
★ 4.0k
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 24 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
1
vote
2
replies
921
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 1 day ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
353
views
GSVA error
GSVA
10 days ago • updated 9 days ago
Alex
• 0
1
vote
3
replies
74
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 hours ago by
Michael Love
41k • written 17 hours ago by
andrebolerbarros
▴ 20
1
vote
1
reply
160
views
Differentially expressed genes in monocle pseudotime
monocle
updated 8 days ago by
Gordon Smyth
50k • written 10 days ago by
kthapa
• 0
1
vote
2
replies
214
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
29 days ago
Mj.A.
• 0
1
vote
0
replies
195
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
5 days ago
BioinfGuru
▴ 30
1
vote
1
reply
53
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
fernanda.backsouza
▴ 10
1
vote
1
reply
135
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago
Layal
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago
hemantcnaik
• 0
1
vote
4
replies
411
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by
Gordon Smyth
50k • written 21 days ago by
jari.karppinen
• 0
1
vote
6
replies
401
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 21 days ago by
Michael Love
41k • written 21 days ago by
RL
• 0
1
vote
2
replies
110
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
8 days ago
Ana
• 0
1
vote
5
replies
298
views
fgsea fork
fgsea
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
yimjohns
• 0
1
vote
2
replies
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
2
replies
163
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
23 days ago • updated 22 days ago
Seongsu
• 0
0
votes
1
reply
115
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
1
reply
98
views
what is the sampleFiles
chipseq
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
zhulin
• 0
0
votes
1
reply
59
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 8 hours ago by
swbarnes2
★ 1.3k • written 17 hours ago by
winwater0928
• 0
0
votes
3
replies
126
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
prity6459
• 0
0
votes
1
reply
211
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 20 days ago by
Tim Peters
▴ 170 • written 21 days ago by
Kim
• 0
0
votes
0
replies
57
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
9 days ago
Henry
▴ 10
0
votes
0
replies
82
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
13 days ago
communication
• 0
0
votes
0
replies
39
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
3 days ago
vaxahey107
• 0
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago
fr8712ca-s
• 0
0
votes
7
replies
346
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
25 days ago • updated 22 days ago
needNGS
• 0
0
votes
2
replies
324
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
4 weeks ago • updated 22 days ago
Gordon
• 0
0
votes
1
reply
154
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
0
votes
4
replies
199
views
Storing directories inside an ExperimentHub package?
ExperimentHub
14 days ago • updated 13 days ago
Tim Barry
• 0
0
votes
1
reply
117
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Karen
• 0
207 results • Page
2 of 5
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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