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15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago
Chris
• 0
12
votes
12
replies
749
views
Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by
Robert Castelo
★ 3.3k • written 4 days ago by
Chris
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 6 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 6 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 2 days ago
shepherl
3.8k
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
5
replies
395
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 1 day ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 6 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
9
replies
849
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
14 days ago • updated 6 days ago
Chris
• 0
4
votes
6
replies
322
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
4
votes
8
replies
338
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 6 days ago by
Peter Hickey
▴ 740 • written 13 days ago by
Juan Higareda
• 0
3
votes
3
replies
282
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 16 days ago by
Netanel
• 0
3
votes
2
replies
149
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
fernanda.backsouza
▴ 10
3
votes
3
replies
166
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
12 days ago • updated 6 days ago
jacques.imbert
• 0
3
votes
3
replies
145
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
3
votes
1
reply
112
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Shaimaa Gamal
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
2
votes
5
replies
694
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
136
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 5 days ago by
James W. MacDonald
65k • written 6 days ago by
sansan
• 0
2
votes
1
reply
152
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
2
votes
3
replies
85
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 10 hours ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
2
votes
5
replies
125
views
get BM error
ensembldb
updated 8 hours ago by
James W. MacDonald
65k • written 17 hours ago by
Fara
• 0
1
vote
0
replies
31
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
14 hours ago
ATpoint
★ 4.0k
1
vote
3
replies
74
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 hours ago by
Michael Love
41k • written 16 hours ago by
andrebolerbarros
▴ 20
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
13
replies
233
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 3 hours ago
fernanda.backsouza
▴ 10
1
vote
2
replies
179
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago
Le
• 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
2
replies
919
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
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
58
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
1
vote
4
replies
126
views
minfi::read.metharray.exp
minfiData
minfi
updated 16 hours ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 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
1
vote
3
replies
809
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 14 hours ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
0
votes
4
replies
119
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
0
replies
14
views
ATACseq merge peaks
DiffBind
7 hours ago
Shloka
• 0
0
votes
1
reply
48
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 3 hours ago by
Michael Love
41k • written 7 hours ago by
kcarey
• 0
0
votes
1
reply
112
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
quanah.hudson
• 0
0
votes
1
reply
78
views
Input Question for deseq.r
RSeqAn
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
Nina
• 0
0
votes
1
reply
110
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
95
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
85
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
1
reply
87
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
ishij9717
• 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
81
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Alessia
• 0
0
votes
0
replies
85
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
0
votes
3
replies
221
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 12 days ago by
schlumbohm
• 0
76 results • Page
1 of 2
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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