0
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0
replies
12
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
1 hour ago • updated 49 minutes ago Chris • 0
0
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0
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17
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
6 hours ago robersy • 0
2
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2
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74
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fgsea significant result
fgsea
1 day ago • updated 8 hours ago Chris • 0
1
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2
replies
319
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 2 days ago by 50k • written 2 days ago by • 0
2
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3
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99
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package goseq seems to be not available on the latest version of R
goseq
updated 2 hours ago by 50k • written 2 days ago by ▴ 20
2
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3
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150
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Too many significant genes when integrating gtex and tcga
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updated 17 hours ago by ★ 4.1k • written 2 days ago by • 0
1
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1
reply
69
views
Handling multiple differential expression comparisons
DESeq2
updated 15 hours ago by 41k • written 2 days ago by ▴ 10
0
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0
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46
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dba.plotProfile() plotting and interpretation
DiffBind
2 days ago Henry ▴ 10
0
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6
replies
189
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Once again a "Model matrix not full rank"
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updated 1 day ago by ★ 1.3k • written 3 days ago by ▴ 130
3
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4
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427
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 2 hours ago by • 0 • written 3 days ago by ▴ 10
0
votes
1
reply
97
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 3 days ago by 50k • written 3 days ago by • 0
0
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1
reply
93
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Gene-by-sample covariates in limma
Metabolomics limma
updated 3 days ago by 50k • written 3 days ago by • 0
0
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0
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42
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flowStats for CyTOF
flowStats
3 days ago tholmes • 0
0
votes
2
replies
93
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
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0
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44
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
3 days ago yvonneh • 0
0
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0
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39
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
3 days ago Ian D. ▴ 70
0
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1
reply
57
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 3 days ago by • 0
0
votes
2
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127
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Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago kcarey • 0
0
votes
3
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131
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
1
reply
131
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
3
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0
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66
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News: Bioconductor 3.19 is Released!
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4 days ago shepherl 3.9k
0
votes
0
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84
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Empty table plot using plotGseaTable()
fgsea
4 days ago • updated 2 days ago Chris • 0
0
votes
3
replies
149
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Store output of matchPWM()
biostrings Biostrings
updated 4 days ago by 65k • written 4 days ago by ▴ 70
0
votes
2
replies
124
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
4 days ago • updated 3 days ago Ian D. ▴ 70
0
votes
2
replies
220
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
5 days ago • updated 4 days ago Yveto • 0
0
votes
3
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242
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
3
votes
4
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199
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Help with error using camera() in limma
CAMERA limma
5 days ago Chris • 0
1
vote
1
reply
103
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
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0
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59
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News: BioC2024 deadlines approaching
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5 days ago Maria Doyle ▴ 70
0
votes
1
reply
101
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putting my own expression data in deseq2
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
2
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119
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Timecourse RNASeq analysis
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5 days ago • updated 2 days ago Aurora • 0
0
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1
reply
81
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 5 days ago by 3.9k • written 5 days ago by • 0
0
votes
1
reply
223
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 5 days ago by 65k • written 5 days ago by • 0
0
votes
1
reply
100
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
2
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2
replies
189
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 days ago Chris • 0
0
votes
0
replies
70
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
6 days ago Chris • 0
0
votes
3
replies
235
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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 5 days ago by 65k • written 6 days ago by • 0
3
votes
3
replies
223
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
1
vote
1
reply
123
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 9 days ago by ▴ 40 • written 9 days ago by ★ 1.5k
1
vote
3
replies
214
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 10 days ago by • 0
1
vote
7
replies
325
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
10 days ago • updated 9 days ago pl23 • 0
2
votes
9
replies
388
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 10 days ago by • 0
0
votes
0
replies
122
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
10 days ago • updated 2 days ago glaciya2018 • 0
0
votes
2
replies
205
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PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
152
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
132
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ATACseq merge peaks
DiffBind
updated 9 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
0
replies
86
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
11 days ago • updated 6 days ago Sara • 0
0
votes
0
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82
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
11 days ago Dario Strbenac ★ 1.5k
1
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2
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
11 days ago • updated 10 days ago ATpoint ★ 4.1k
1
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3
replies
210
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Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
45,619 results • Page 1 of 913
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Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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