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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
754
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
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
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
5
replies
396
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
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
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
853
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
324
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
4
votes
8
replies
341
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
167
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
2
replies
150
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
149
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
3
votes
3
replies
282
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 16 days ago by
Netanel
• 0
2
votes
2
replies
137
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
5
replies
695
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
5
replies
133
views
get BM error
ensembldb
updated 13 hours ago by
James W. MacDonald
65k • written 23 hours ago by
Fara
• 0
2
votes
3
replies
91
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 16 hours ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
2
votes
1
reply
156
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
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 2 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
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
179
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago
Le
• 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
13
replies
241
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 9 hours ago
fernanda.backsouza
▴ 10
1
vote
0
replies
196
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
63
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
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
1
vote
4
replies
127
views
minfi::read.metharray.exp
minfiData
minfi
updated 22 hours ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
1
vote
3
replies
810
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 20 hours ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
1
vote
0
replies
34
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
19 hours ago
ATpoint
★ 4.0k
1
vote
3
replies
77
views
Different Shrunk Log2FC according with reference
DESeq2
updated 17 hours ago by
Michael Love
41k • written 21 hours ago by
andrebolerbarros
▴ 20
0
votes
0
replies
14
views
ATACseq merge peaks
DiffBind
12 hours ago
Shloka
• 0
0
votes
1
reply
64
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 8 hours ago by
Michael Love
41k • written 12 hours ago by
kcarey
• 0
0
votes
2
replies
84
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 2 hours ago
shuwangxinze1996
• 0
0
votes
0
replies
8
views
PCA plot suggestions
DESeq2
PCAtools
2 hours ago
Aaliya
• 0
0
votes
8
replies
160
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 31 minutes ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 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
111
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
96
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
86
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
88
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
82
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
86
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
76 results • Page
1 of 2
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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