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1
vote
2
replies
288
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
17 days ago • updated 16 days ago
Yveto
• 0
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
HAK
• 0
4
votes
0
replies
135
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
16 days ago
shepherl
3.9k
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
28 days ago • updated 16 days ago
Chris
▴ 10
1
vote
4
replies
529
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 16 days ago
JKim
• 0
3
votes
4
replies
260
views
Help with error using camera() in limma
CAMERA
limma
18 days ago • updated 17 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 17 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 17 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
262
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
SSSJec
• 0
0
votes
3
replies
274
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 17 days ago by
James W. MacDonald
65k • written 19 days ago by
SSSJec
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 18 days ago
Chris
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 18 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
188
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 18 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
1
vote
1
reply
156
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
marcusn
• 0
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
0
votes
0
replies
93
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
18 days ago
Maria Doyle
▴ 70
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 18 days ago by
shepherl
3.9k • written 18 days ago by
bounlu
• 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
2
votes
2
replies
234
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago
Chris
▴ 10
0
votes
0
replies
94
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
19 days ago • updated 18 days ago
Chris
▴ 10
0
votes
4
replies
262
views
Minfi - estimatecellscount
min
minfi
updated 19 days ago by
James W. MacDonald
65k • written 7 weeks ago by
clacarion
• 0
3
votes
3
replies
269
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 19 days ago by
ATpoint
★ 4.1k • written 19 days ago by
bioinf
▴ 10
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
24 days ago • updated 19 days ago
Sara
• 0
1
vote
1
reply
153
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by
Leo Lahti
▴ 40 • written 22 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
357
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago
pl23
• 0
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2
PCAtools
updated 22 days ago by
Michael Love
42k • written 23 days ago by
Aaliya
• 0
1
vote
2
replies
740
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 22 days ago
Patadù
▴ 10
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 22 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
1
vote
4
replies
356
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago
winwater0928
• 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
Alexandre
• 0
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 22 days ago by
James W. MacDonald
65k • written 24 days ago by
bandconductor
• 0
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
24 days ago • updated 23 days ago
ATpoint
★ 4.1k
0
votes
2
replies
265
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
25 days ago • updated 23 days ago
shuwangxinze1996
• 0
0
votes
8
replies
385
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 23 days ago by
swbarnes2
★ 1.4k • written 25 days ago by
Aaliya
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
2
votes
13
replies
479
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
26 days ago • updated 23 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
305
views
get BM error
ensembldb
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
Fara
• 0
0
votes
5
replies
324
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 24 days ago by
James W. MacDonald
65k • written 26 days ago by
Gayatri
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
24 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
891
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 24 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
229
views
minfi::read.metharray.exp
minfiData
minfi
updated 24 days ago by
Basti
▴ 780 • written 26 days ago by
clacarion
• 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
0
votes
7
replies
746
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 24 days ago
shepherl
3.9k
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 25 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
82
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
25 days ago
info
▴ 10
3
votes
3
replies
251
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 25 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
0
votes
7
replies
362
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 25 days ago
hortense96
• 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 25 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
182 results • Page
3 of 4
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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