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Votes
0
votes
2
replies
138
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
19 days ago
prity6459
• 0
1
vote
2
replies
164
views
Error in champ.load(): The following specified files do not exist
ChAMP
21 days ago • updated 20 days ago
Sherin
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
21 days ago • updated 12 days ago
ussarizona
▴ 10
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2
PCAtools
updated 12 days ago by
Michael Love
42k • written 13 days ago by
Aaliya
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
28 days ago • updated 19 days ago
Weiqian
▴ 10
0
votes
2
replies
132
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
8 days ago • updated 5 days ago
Aurora
• 0
1
vote
2
replies
221
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 days ago
Le
• 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
kys91240
• 0
0
votes
2
replies
153
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
7 days ago • updated 6 days ago
kcarey
• 0
2
votes
2
replies
208
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
9 days ago
Chris
• 0
1
vote
2
replies
343
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Kim
• 0
0
votes
2
replies
172
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 16 days ago by
taur.vil
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 22 days ago
Henry
▴ 10
1
vote
2
replies
313
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 5 days ago
Kim
• 0
1
vote
2
replies
145
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
22 days ago
Ana
• 0
0
votes
2
replies
254
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
15 days ago • updated 13 days ago
shuwangxinze1996
• 0
0
votes
2
replies
259
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 19 days ago
isaac.vock
• 0
2
votes
2
replies
393
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
1
vote
2
replies
242
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
0
votes
2
replies
117
views
DESeq2 v1.35.0
DESeq2
updated 6 days ago by
Michael Love
42k • written 6 days ago by
Espresso
• 0
2
votes
2
replies
199
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
26 days ago
julia_mcdonough
• 0
2
votes
2
replies
193
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
sansan
• 0
3
votes
2
replies
219
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 16 days ago by
Guido Hooiveld
★ 3.9k • written 19 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
215
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
19 days ago • updated 16 days ago
catv
• 0
1
vote
1
reply
84
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 2 days ago by
Michael Love
42k • written 2 days ago by
mat149
▴ 70
0
votes
1
reply
123
views
what is the sampleFiles
chipseq
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
zhulin
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 20 days ago by
Michael Love
42k • written 20 days ago by
09191919
• 0
0
votes
1
reply
111
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 6 days ago by
Gordon Smyth
50k • written 6 days ago by
c53aba27
• 0
0
votes
1
reply
143
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 22 days ago by
James W. MacDonald
65k • written 25 days ago by
tian.liu0720
• 0
3
votes
1
reply
756
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
1
vote
1
reply
123
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 8 days ago by
Michael Love
42k • written 8 days ago by
marcusn
• 0
3
votes
1
reply
180
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 19 days ago by
Gordon Smyth
50k • written 20 days ago by
Shaimaa Gamal
• 0
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
i.sudbery
▴ 40
0
votes
1
reply
143
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 28 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Merav
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 25 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 26 days ago by
hemantcnaik
• 0 • written 26 days ago by
Sahar
• 0
1
vote
1
reply
181
views
Citation for edgeR user guide
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
k___
▴ 30
0
votes
1
reply
115
views
putting my own expression data in deseq2
DESeq2
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Dev
• 0
0
votes
1
reply
47
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 1 day ago by
shepherl
3.9k • written 1 day ago by
cyril.dalmasso
• 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
28 days ago • updated 27 days ago
Shefali
• 0
0
votes
1
reply
82
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 6 days ago by
4r-rtg
• 0
0
votes
1
reply
164
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 24 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
Lucie
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 14 days ago by
Michael Love
42k • written 14 days ago by
kcarey
• 0
0
votes
1
reply
141
views
ATACseq merge peaks
DiffBind
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Shloka
• 0
0
votes
1
reply
152
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
quanah.hudson
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 20 days ago by
Michael Love
42k • written 20 days ago by
ishij9717
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Nina
• 0
0
votes
1
reply
147
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 22 days ago by
kamryncole1963
• 0 • written 27 days ago by
Sara
• 0
0
votes
1
reply
129
views
FDR via q-value
qvalue
updated 16 days ago by
James W. MacDonald
65k • written 19 days ago by
John
• 0
3
votes
1
reply
87
views
How to save the DEXSeq results
DEXSeq
updated 2 days ago by
Michael Love
42k • written 2 days ago by
Sara
• 0
202 results • Page
3 of 5
Recent ...
Replies
Comment: EGSEA usage with microarray data (with vooma)?
by
Chris
• 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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42k
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• 0
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to
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▴ 10
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DevelopingHippo
• 0
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Robert Castelo
★ 3.3k
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