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0
votes
0
replies
62
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 days ago
yvonneh
• 0
0
votes
0
replies
59
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 days ago
Ian D.
▴ 70
0
votes
1
reply
95
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 8 days ago by
4r-rtg
• 0
0
votes
3
replies
171
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
james.zhang20
• 0
0
votes
2
replies
174
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 17 days ago by
taur.vil
• 0
1
vote
2
replies
253
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
9 days ago • updated 8 days ago
Yveto
• 0
0
votes
3
replies
267
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 days ago by
Michael Love
42k • written 9 days ago by
HAK
• 0
4
votes
0
replies
100
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
8 days ago
shepherl
3.9k
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
20 days ago • updated 8 days ago
Chris
• 0
0
votes
3
replies
183
views
Store output of matchPWM()
biostrings
Biostrings
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
mat149
▴ 70
1
vote
4
replies
493
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 8 days ago
JKim
• 0
3
votes
4
replies
235
views
Help with error using camera() in limma
CAMERA
limma
9 days ago
Chris
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 9 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 9 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
241
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
SSSJec
• 0
0
votes
3
replies
255
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 9 days ago by
James W. MacDonald
65k • written 11 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
5 weeks ago • updated 9 days ago
Chris
• 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 9 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 22 days ago by
Alessia
• 0
1
vote
1
reply
132
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 10 days ago by
Michael Love
42k • written 10 days ago by
marcusn
• 0
0
votes
1
reply
120
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Agung
• 0
0
votes
0
replies
80
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
10 days ago
Maria Doyle
▴ 70
0
votes
1
reply
106
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 10 days ago by
shepherl
3.9k • written 10 days ago by
bounlu
• 0
0
votes
1
reply
121
views
putting my own expression data in deseq2
DESeq2
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Dev
• 0
2
votes
2
replies
214
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
10 days ago
Chris
• 0
0
votes
0
replies
83
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
11 days ago • updated 10 days ago
Chris
• 0
0
votes
4
replies
255
views
Minfi - estimatecellscount
min
minfi
updated 11 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
3
votes
3
replies
247
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
bioinf
▴ 10
0
votes
0
replies
93
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
16 days ago • updated 11 days ago
Sara
• 0
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 13 days ago by
Leo Lahti
▴ 40 • written 14 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
338
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
14 days ago • updated 13 days ago
pl23
• 0
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2
PCAtools
updated 13 days ago by
Michael Love
42k • written 15 days ago by
Aaliya
• 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
23 days ago • updated 14 days ago
ussarizona
▴ 10
1
vote
3
replies
235
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 14 days ago by
Michael Love
42k • written 14 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
143
views
ATACseq merge peaks
DiffBind
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Shloka
• 0
1
vote
4
replies
343
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago
winwater0928
• 0
2
votes
9
replies
405
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 14 days ago by
James W. MacDonald
65k • written 15 days ago by
Alexandre
• 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 14 days ago by
James W. MacDonald
65k • written 16 days ago by
bandconductor
• 0
1
vote
2
replies
166
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
16 days ago • updated 15 days ago
ATpoint
★ 4.1k
0
votes
2
replies
259
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
17 days ago • updated 15 days ago
shuwangxinze1996
• 0
0
votes
8
replies
361
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 15 days ago by
swbarnes2
★ 1.4k • written 16 days ago by
Aaliya
• 0
0
votes
1
reply
157
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 15 days ago by
Michael Love
42k • written 15 days ago by
kcarey
• 0
2
votes
13
replies
443
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
18 days ago • updated 15 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
279
views
get BM error
ensembldb
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
Fara
• 0
0
votes
5
replies
307
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 16 days ago by
James W. MacDonald
65k • written 18 days ago by
Gayatri
• 0
0
votes
0
replies
89
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
16 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
222
views
Different Shrunk Log2FC according with reference
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
872
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 16 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
213
views
minfi::read.metharray.exp
minfiData
minfi
updated 16 days ago by
Basti
▴ 780 • written 17 days ago by
clacarion
• 0
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by
Michael Love
42k • written 16 days ago by
i.sudbery
▴ 40
1,000 results • Page
2 of 20
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Replies
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Comment: deseq2 results
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