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1
vote
4
replies
360
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
26 days ago • updated 24 days ago
winwater0928
• 0
1
vote
2
replies
137
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago
Daniel
• 0
1
vote
1
reply
158
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 20 days ago by
Michael Love
42k • written 20 days ago by
marcusn
• 0
1
vote
2
replies
87
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 3 hours ago
Anna
• 0
1
vote
2
replies
206
views
Citation for edgeR user guide
edgeR
written 26 days ago by
k___
▴ 30
1
vote
4
replies
532
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 18 days ago
JKim
• 0
1
vote
3
replies
256
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Ashley
• 0
1
vote
2
replies
1.0k
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 27 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
750
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 24 days ago
Patadù
▴ 10
1
vote
5
replies
525
views
Can't post a question containing code?
Bioconductor
updated 9 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 12 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
26 days ago • updated 25 days ago
ATpoint
★ 4.1k
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 26 days ago by
Basti
▴ 780 • written 28 days ago by
clacarion
• 0
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
19 days ago • updated 18 days ago
Yveto
• 0
1
vote
2
replies
285
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
11 days ago • updated 10 days ago
Dylan.Sheerin
• 0
1
vote
0
replies
69
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
6 days ago
Aleena
▴ 30
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by
Michael Love
42k • written 17 days ago by
Zainab
▴ 10
1
vote
2
replies
216
views
Improving the design matrices vignette in RNAseq123
RNAseq123
28 days ago • updated 14 days ago
Lluís Revilla Sancho
▴ 730
1
vote
1
reply
135
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
fernanda.backsouza
▴ 10
1
vote
0
replies
337
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 6 days ago
shepherl
3.9k
1
vote
1
reply
154
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 23 days ago by
Leo Lahti
▴ 40 • written 24 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
306
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 18 days ago by
angelathuynh5
• 0
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
Kim
• 0
1
vote
2
replies
252
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
6 days ago • updated 3 days ago
BioinfGuru
▴ 30
1
vote
2
replies
105
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
5 days ago
Patadù
▴ 10
1
vote
3
replies
892
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 26 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
3
replies
256
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 24 days ago by
Michael Love
42k • written 24 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
378
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 16 days ago
Kim
• 0
1
vote
3
replies
238
views
Different Shrunk Log2FC according with reference
DESeq2
updated 26 days ago by
Michael Love
42k • written 26 days ago by
andrebolerbarros
▴ 20
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago
pl23
• 0
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2
PCAtools
updated 24 days ago by
Michael Love
42k • written 25 days ago by
Aaliya
• 0
0
votes
2
replies
174
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Espresso
• 0
0
votes
1
reply
119
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 13 days ago by
shepherl
3.9k • written 13 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
61
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
6 days ago
Researcher
• 0
0
votes
1
reply
103
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 6 days ago by
Michael Love
42k • written 7 days ago by
piemmea
• 0
0
votes
3
replies
190
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 20 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago
Ian D.
▴ 70
0
votes
2
replies
141
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 6 days ago by
zhouwanding
▴ 10 • written 8 days ago by
Seungmin
• 0
0
votes
2
replies
753
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 4 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 3 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
0
votes
2
replies
268
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
27 days ago • updated 25 days ago
shuwangxinze1996
• 0
0
votes
1
reply
138
views
putting my own expression data in deseq2
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 20 days ago by
Dev
• 0
0
votes
3
replies
126
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 5 days ago by
Michael Love
42k • written 5 days ago by
Kasper
• 0
0
votes
0
replies
96
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
0
votes
7
replies
366
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 27 days ago
hortense96
• 0
0
votes
0
replies
101
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
26 days ago • updated 21 days ago
Sara
• 0
0
votes
0
replies
87
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
27 days ago
info
▴ 10
0
votes
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
c53aba27
• 0
0
votes
2
replies
215
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
18 days ago • updated 17 days ago
kcarey
• 0
0
votes
4
replies
378
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 8 days ago by
Ziliang
• 0 • written 19 days ago by
Ian D.
▴ 70
169 results • Page
2 of 4
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm
by
Michael Love
42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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