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14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 6 days ago
Chris
• 0
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 5 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
4
votes
9
replies
435
views
Memory errors using read.bismark?
dmrseq
bsseq
26 days ago • updated 10 hours ago
Juan Higareda
• 0
4
votes
2
replies
544
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
5 days ago • updated 1 day ago
gene_bioconductor
▴ 10
3
votes
4
replies
151
views
Help with running egsea()
EGSEA
1 day ago • updated 5 hours ago
Chris
• 0
3
votes
0
replies
83
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
6 days ago
shepherl
3.9k
3
votes
4
replies
170
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 2 hours ago by
Gordon Smyth
50k • written 2 days ago by
Chris
• 0
3
votes
2
replies
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 57 minutes ago by
nbay13
• 0 • written 5.6 years ago by
CantExitVIM
▴ 10
3
votes
1
reply
79
views
How to save the DEXSeq results
DEXSeq
updated 1 day ago by
Michael Love
42k • written 1 day ago by
Sara
• 0
2
votes
3
replies
168
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 day ago by
Gordon Smyth
50k • written 4 days ago by
Patrycja
▴ 20
2
votes
2
replies
142
views
fgsea significant result
fgsea
3 days ago • updated 2 days ago
Chris
• 0
2
votes
3
replies
182
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Reza
• 0
1
vote
2
replies
191
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 1 day ago
Lluís Revilla Sancho
▴ 730
1
vote
2
replies
237
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
1
vote
2
replies
311
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 4 days ago
Kim
• 0
1
vote
2
replies
337
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
Kim
• 0
1
vote
1
reply
107
views
Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by
Michael Love
42k • written 4 days ago by
Zainab
▴ 10
1
vote
4
replies
483
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 6 days ago
JKim
• 0
1
vote
1
reply
77
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 1 day ago by
Michael Love
42k • written 1 day ago by
mat149
▴ 70
1
vote
0
replies
207
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 1 day ago
shepherl
3.9k
1
vote
3
replies
229
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 1 day ago by
Hervé Pagès
16k • written 2 days ago by
robersy
• 0
1
vote
1
reply
53
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 9 hours ago by
James W. MacDonald
65k • written 10 hours ago by
Abbey
• 0
1
vote
1
reply
61
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 8 hours ago by
James W. MacDonald
65k • written 9 hours ago by
zzrammal
• 0
1
vote
2
replies
169
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
6 days ago • updated 1 hour ago
angelathuynh5
• 0
0
votes
0
replies
56
views
flowStats for CyTOF
flowStats
5 days ago
tholmes
• 0
0
votes
1
reply
62
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 13 hours ago by
James W. MacDonald
65k • written 18 hours ago by
e1271094
• 0
0
votes
2
replies
112
views
DESeq2 v1.35.0
DESeq2
updated 5 days ago by
Michael Love
42k • written 5 days ago by
Espresso
• 0
0
votes
5
replies
2.8k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 2 days ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
51
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
5 days ago
yvonneh
• 0
0
votes
0
replies
46
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
5 days ago
Ian D.
▴ 70
0
votes
3
replies
151
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
james.zhang20
• 0
0
votes
3
replies
256
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by
Michael Love
42k • written 7 days ago by
HAK
• 0
0
votes
2
replies
139
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 days ago • updated 5 days ago
Ian D.
▴ 70
0
votes
1
reply
77
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 5 days ago by
4r-rtg
• 0
0
votes
3
replies
162
views
Store output of matchPWM()
biostrings
Biostrings
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
mat149
▴ 70
0
votes
3
replies
110
views
Couldn't connect to server while using "pathways"
graphite
updated 1 day ago by
Michael Love
42k • written 1 day ago by
fduguchunhui
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 1 day ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
34
replies
2.6k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 1 day ago
Poonam
• 0
0
votes
0
replies
23
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
1 day ago
Dinesh
• 0
0
votes
1
reply
108
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
c53aba27
• 0
0
votes
1
reply
123
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
z_bahari
• 0
0
votes
2
replies
149
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago
kcarey
• 0
0
votes
0
replies
129
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
12 days ago • updated 4 days ago
glaciya2018
• 0
0
votes
2
replies
128
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
7 days ago • updated 4 days ago
Aurora
• 0
0
votes
0
replies
68
views
dba.plotProfile() plotting and interpretation
DiffBind
4 days ago
Henry
▴ 10
0
votes
2
replies
170
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 15 days ago by
taur.vil
• 0
0
votes
0
replies
95
views
Empty table plot using plotGseaTable()
fgsea
6 days ago • updated 4 days ago
Chris
• 0
0
votes
1
reply
36
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 14 hours ago by
shepherl
3.9k • written 15 hours ago by
cyril.dalmasso
• 0
0
votes
6
replies
222
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 3 days ago by
swbarnes2
★ 1.3k • written 5 days ago by
arfranco
▴ 130
50 results • Page
1 of 1
Recent ...
Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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