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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
3 minutes ago • updated just now
Alexandre
• 0
0
votes
0
replies
19
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
4 hours ago
glaciya2018
• 0
1
vote
2
replies
64
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 day ago • updated 4 hours ago
ATpoint
★ 4.0k
0
votes
0
replies
22
views
PCA plot suggestions
DESeq2
PCAtools
9 hours ago
Aaliya
• 0
0
votes
1
reply
69
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 15 hours ago by
Michael Love
41k • written 19 hours ago by
kcarey
• 0
0
votes
0
replies
16
views
ATACseq merge peaks
DiffBind
19 hours ago
Shloka
• 0
0
votes
0
replies
15
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
21 hours ago
Sara
• 0
2
votes
5
replies
139
views
get BM error
ensembldb
updated 20 hours ago by
James W. MacDonald
65k • written 1 day ago by
Fara
• 0
2
votes
3
replies
100
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 22 hours ago by
James W. MacDonald
65k • written 1 day ago by
bandconductor
• 0
0
votes
0
replies
25
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
23 hours ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
83
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 hours ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
2
replies
83
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 5 hours ago
winwater0928
• 0
2
votes
1
reply
163
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
1
reply
69
views
Citation for edgeR user guide
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
k___
▴ 30
0
votes
7
replies
610
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 1 day ago
shepherl
3.8k
1
vote
1
reply
55
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
0
votes
8
replies
202
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
25
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
1 day ago
info
▴ 10
1
vote
4
replies
129
views
minfi::read.metharray.exp
minfiData
minfi
updated 1 day ago by
Basti
▴ 780 • written 2 days ago by
clacarion
• 0
0
votes
2
replies
104
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 6 hours ago
shuwangxinze1996
• 0
1
vote
2
replies
924
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
0
votes
1
reply
87
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
taur.vil
• 0
3
votes
3
replies
154
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
1
vote
4
replies
142
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
0
votes
1
reply
80
views
FDR via q-value
qvalue
updated 2 days ago by
James W. MacDonald
65k • written 5 days ago by
John
• 0
0
votes
5
replies
208
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 22 hours ago by
James W. MacDonald
65k • written 3 days ago by
Gayatri
• 0
0
votes
2
replies
151
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
5 days ago • updated 3 days ago
catv
• 0
0
votes
0
replies
41
views
Improving the design matrices vignette in RNAseq123
RNAseq123
3 days ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
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
1
vote
13
replies
244
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 15 hours ago
fernanda.backsouza
▴ 10
0
votes
0
replies
39
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
4 days ago
vaxahey107
• 0
12
votes
12
replies
757
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
0
votes
0
replies
61
views
I am trying to detect alternative splicing.
ASpli
4 days ago
Sebashish
• 0
3
votes
2
replies
154
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 5 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
101
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 5 days ago by
James W. MacDonald
65k • written 5 days ago by
bas_work
▴ 30
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
1
vote
0
replies
198
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
6 days ago • updated 5 days ago
BioinfGuru
▴ 30
4
votes
6
replies
325
views
FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago
Jonathan
▴ 10
0
votes
2
replies
90
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 days ago
prity6459
• 0
0
votes
3
replies
127
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
prity6459
• 0
3
votes
1
reply
115
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
131
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago
sropri
• 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 7 days ago by
Alessia
• 0
0
votes
1
reply
116
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
0
replies
87
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
0
votes
1
reply
88
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 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 7 days ago by
09191919
• 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
113
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
45,578 results • Page
1 of 912
Recent ...
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
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…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
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?
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