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0
votes
0
replies
17
views
fgsea significant result
fgsea
4 hours ago
Chris
• 0
1
vote
2
replies
306
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
Kim
• 0
0
votes
1
reply
68
views
package goseq seems to be not available on the latest version of R
goseq
updated 4 hours ago by
Gordon Smyth
50k • written 1 day ago by
Patrycja
• 0
2
votes
2
replies
114
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Reza
• 0
0
votes
0
replies
40
views
Handling multiple differential expression comparisons
DESeq2
1 day ago
Zainab
• 0
0
votes
0
replies
36
views
dba.plotProfile() plotting and interpretation
DiffBind
1 day ago
Henry
▴ 10
0
votes
6
replies
171
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 21 hours ago by
swbarnes2
★ 1.3k • written 2 days ago by
arfranco
▴ 130
1
vote
1
reply
236
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
gene_bioconductor
▴ 10
0
votes
1
reply
87
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
z_bahari
• 0
0
votes
1
reply
84
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
c53aba27
• 0
0
votes
0
replies
34
views
flowStats for CyTOF
flowStats
2 days ago
tholmes
• 0
0
votes
2
replies
80
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Espresso
• 0
0
votes
0
replies
40
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
2 days ago
yvonneh
• 0
0
votes
0
replies
33
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago
Ian D.
▴ 70
0
votes
1
reply
45
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by
4r-rtg
• 0
0
votes
2
replies
116
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 2 days ago
kcarey
• 0
0
votes
3
replies
115
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
james.zhang20
• 0
0
votes
1
reply
122
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
angelathuynh5
• 0
3
votes
0
replies
59
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
3 days ago
shepherl
3.9k
0
votes
0
replies
75
views
Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 1 day ago
Chris
• 0
0
votes
3
replies
142
views
Store output of matchPWM()
biostrings
Biostrings
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
mat149
▴ 70
0
votes
2
replies
116
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
2
replies
213
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
4 days ago • updated 3 days ago
Yveto
• 0
0
votes
3
replies
236
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
HAK
• 0
3
votes
4
replies
192
views
Help with error using camera() in limma
CAMERA
limma
4 days ago
Chris
• 0
1
vote
1
reply
96
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
marcusn
• 0
0
votes
0
replies
56
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
4 days ago
Maria Doyle
▴ 70
0
votes
1
reply
97
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
0
votes
2
replies
111
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
1
reply
74
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 4 days ago by
shepherl
3.9k • written 4 days ago by
bounlu
• 0
0
votes
1
reply
216
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
SSSJec
• 0
0
votes
1
reply
95
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Agung
• 0
2
votes
2
replies
186
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
5 days ago
Chris
• 0
0
votes
0
replies
68
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago
Chris
• 0
0
votes
3
replies
228
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
SSSJec
• 0
3
votes
3
replies
216
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
bioinf
▴ 10
1
vote
1
reply
118
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 8 days ago by
Leo Lahti
▴ 40 • written 8 days ago by
Dario Strbenac
★ 1.5k
1
vote
3
replies
208
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 8 days ago by
Michael Love
41k • written 9 days ago by
JalapenoCornbread
• 0
1
vote
7
replies
309
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago
pl23
• 0
2
votes
9
replies
376
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
Alexandre
• 0
0
votes
0
replies
114
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
9 days ago • updated 1 day ago
glaciya2018
• 0
0
votes
2
replies
200
views
PCA plot suggestions
DESeq2
PCAtools
updated 8 days ago by
Michael Love
41k • written 10 days ago by
Aaliya
• 0
0
votes
1
reply
147
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 10 days ago by
Michael Love
41k • written 10 days ago by
kcarey
• 0
0
votes
1
reply
129
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Shloka
• 0
0
votes
0
replies
83
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
10 days ago • updated 5 days ago
Sara
• 0
0
votes
0
replies
79
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
154
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
10 days ago • updated 9 days ago
ATpoint
★ 4.1k
1
vote
3
replies
206
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
314
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago
winwater0928
• 0
2
votes
5
replies
255
views
get BM error
ensembldb
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Fara
• 0
1,000 results • Page
1 of 20
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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