15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago Chris • 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by • 0 • written 4.6 years ago by ▴ 10
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago Chris • 0
1
vote
7
replies
294
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago pl23 • 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 200 • written 6.7 years ago by ▴ 80
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 6 hours ago by 65k • written 2.3 years ago by • 0
1
vote
4
replies
301
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
3
votes
4
replies
166
views
Help with error using camera() in limma
CAMERA limma
2 days ago Chris • 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min minfi
updated 3 days ago by 65k • written 4 weeks ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 2 days ago by • 0 • written 13.0 years ago by ▴ 10
0
votes
3
replies
207
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 2 days ago by 65k • written 3 days ago by • 0
0
votes
3
replies
43
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
2 hours ago arfranco ▴ 130
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 12 hours ago by ★ 4.1k • written 1 day ago by • 0
3
votes
3
replies
196
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
0
votes
3
replies
217
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
3
replies
109
views
Store output of matchPWM()
biostrings Biostrings
updated 1 day ago by 65k • written 1 day ago by ▴ 70
0
votes
3
replies
154
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by ★ 1.9k • written 14 days ago by • 0
0
votes
2
replies
56
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 10 minutes ago kcarey • 0
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
2
votes
2
replies
168
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago Chris • 0
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 2 days ago by • 0 • written 7.9 years ago by • 0
0
votes
2
replies
192
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
1 day ago • updated 22 hours ago Yveto • 0
0
votes
2
replies
150
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 10 days ago by • 0
0
votes
2
replies
88
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 8 hours ago Ian D. ▴ 70
0
votes
2
replies
47
views
DESeq2 v1.35.0
DESeq2
updated 6 hours ago by 41k • written 7 hours ago by • 0
0
votes
1
reply
86
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
62
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by 3.9k • written 2 days ago by • 0
0
votes
1
reply
85
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
1
reply
29
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 13 hours ago by • 0
0
votes
1
reply
20
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 20 minutes ago by 50k • written 4 hours ago by • 0
1
vote
1
reply
108
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by ▴ 40 • written 6 days ago by ★ 1.5k
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by 50k • written 10 days ago by ▴ 730
0
votes
1
reply
204
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 2 days ago by 65k • written 2 days ago by • 0
1
vote
1
reply
81
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
1
reply
75
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
97
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
0
votes
1
reply
35
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 39 minutes ago by 50k • written 3 hours ago by ▴ 10
0
votes
1
reply
23
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 21 minutes ago by 50k • written 4 hours ago by • 0
3
votes
0
replies
40
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
1 day ago shepherl 3.9k
0
votes
0
replies
45
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
2 days ago Maria Doyle ▴ 70
0
votes
0
replies
55
views
Empty table plot using plotGseaTable()
fgsea
1 day ago Chris • 0
0
votes
0
replies
55
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago Chris • 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 hours ago Ian D. ▴ 70
0
votes
0
replies
16
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
8 hours ago yvonneh • 0
0
votes
0
replies
72
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
8 days ago • updated 3 days ago Sara • 0
0
votes
0
replies
12
views
flowStats for CyTOF
flowStats
6 hours ago tholmes • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
United States, 1 minute ago
France, 4 minutes ago
WEHI, Melbourne, Australia, 9 minutes ago
United States, 54 minutes ago
European Union, 1 hour ago
Traffic: 552 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6