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Views
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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
2
replies
287
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
12 days ago • updated 11 days ago
Dylan.Sheerin
• 0
1
vote
2
replies
90
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 12 hours ago
Anna
• 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
4
replies
532
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 19 days ago
JKim
• 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
1
reply
155
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 24 days ago by
Leo Lahti
▴ 40 • written 24 days ago by
Dario Strbenac
★ 1.5k
1
vote
5
replies
527
views
Can't post a question containing code?
Bioconductor
updated 10 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
1
vote
0
replies
338
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
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 19 days ago by
angelathuynh5
• 0
1
vote
2
replies
755
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 24 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 25 days ago by
JalapenoCornbread
• 0
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
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
0
replies
71
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
6 days ago
Aleena
▴ 30
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
20 days ago • updated 19 days ago
Yveto
• 0
1
vote
2
replies
109
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
5 days ago
Patadù
▴ 10
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
Kim
• 0
1
vote
2
replies
207
views
Citation for edgeR user guide
edgeR
written 27 days ago by
k___
▴ 30
1
vote
1
reply
194
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by
Michael Love
42k • written 17 days ago by
Zainab
▴ 10
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
138
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago
Daniel
• 0
1
vote
2
replies
381
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 17 days ago
Kim
• 0
1
vote
2
replies
254
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
7 days ago • updated 4 days ago
BioinfGuru
▴ 30
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago
pl23
• 0
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
3
replies
256
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Ashley
• 0
1
vote
4
replies
362
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
217
views
Improving the design matrices vignette in RNAseq123
RNAseq123
28 days ago • updated 14 days ago
Lluís Revilla Sancho
▴ 730
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
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Espresso
• 0
0
votes
2
replies
956
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 10 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
51
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 11 hours ago by
James W. MacDonald
65k • written 19 hours ago by
ttt
• 0
0
votes
1
reply
120
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
104
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
145
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 5 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
140
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
0
replies
9
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
2 hours ago
Tim Barry
• 0
0
votes
3
replies
131
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 5 days ago by
Michael Love
42k • written 6 days ago by
Kasper
• 0
0
votes
2
replies
171
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
20 days ago • updated 17 days ago
Aurora
• 0
0
votes
1
reply
38
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 16 hours ago by
ATpoint
★ 4.1k • written 17 hours ago by
V_Vibes
• 0
0
votes
0
replies
97
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
172 results • Page
2 of 4
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
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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3.9k
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