15
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23
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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
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19
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2.4k
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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
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17
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1.1k
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Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago Chris • 0
1
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7
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294
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago pl23 • 0
8
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6
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1.7k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 200 • written 6.7 years ago by ▴ 80
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6
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2.8k
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 9 hours ago by 65k • written 2.3 years ago by • 0
1
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4
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456
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
1
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4
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301
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
0
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4
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237
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Minfi - estimatecellscount
min minfi
updated 3 days ago by 65k • written 4 weeks ago by • 0
3
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4
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166
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Help with error using camera() in limma
CAMERA limma
2 days ago Chris • 0
0
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3
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1.5k
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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
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209
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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
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3
replies
54
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Once again a "Model matrix not full rank"
DESeq2 design coldata
5 hours ago arfranco ▴ 130
0
votes
3
replies
93
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 hours ago by ★ 4.1k • written 1 day ago by • 0
3
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3
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197
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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
219
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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
113
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Store output of matchPWM()
biostrings Biostrings
updated 1 day ago by 65k • written 1 day ago by ▴ 70
0
votes
3
replies
155
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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
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2
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49
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DESeq2 v1.35.0
DESeq2
updated 9 hours ago by 41k • written 10 hours ago by • 0
1
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2
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695
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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
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PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
2
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2
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169
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago Chris • 0
2
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2
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1.0k
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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
194
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
2 days ago • updated 1 day ago Yveto • 0
0
votes
2
replies
150
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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
90
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 11 hours ago Ian D. ▴ 70
0
votes
2
replies
69
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Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 3 hours ago kcarey • 0
0
votes
1
reply
86
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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
63
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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
87
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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
30
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 16 hours ago by • 0
0
votes
1
reply
113
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 hour ago by 50k • written 7 hours ago by ▴ 10
1
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1
reply
108
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by ▴ 40 • written 6 days ago by ★ 1.5k
0
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1
reply
114
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ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
1
reply
205
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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
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1
reply
81
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
1
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1
reply
151
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Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by 50k • written 10 days ago by ▴ 730
0
votes
1
reply
75
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
100
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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
40
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Gene-by-sample covariates in limma
Metabolomics limma
updated 3 hours ago by 50k • written 8 hours ago by • 0
0
votes
1
reply
33
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 3 hours ago by 50k • written 8 hours ago by • 0
3
votes
0
replies
40
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
1 day ago shepherl 3.9k
0
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0
replies
45
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
2 days ago Maria Doyle ▴ 70
0
votes
0
replies
55
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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
11 hours ago Ian D. ▴ 70
0
votes
0
replies
19
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
11 hours ago yvonneh • 0
0
votes
0
replies
72
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
8 days ago • updated 3 days ago Sara • 0
0
votes
0
replies
14
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flowStats for CyTOF
flowStats
9 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
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