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23
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NEED FOR NESSASORY HELP
RNASeqData edgeR
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25
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Gene-by-sample covariates in limma
Metabolomics limma
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0
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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updated 13 minutes ago by 50k • written 5 hours ago by ▴ 10
0
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3
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49
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Once again a "Model matrix not full rank"
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3 hours ago arfranco ▴ 130
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flowStats for CyTOF
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7 hours ago tholmes • 0
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2
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48
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updated 7 hours ago by 41k • written 8 hours ago by • 0
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DiffBind: no peaks in DBA object
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9 hours ago yvonneh • 0
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How to create consensus peak sets for each group to use in DiffBind?
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9 hours ago Ian D. ▴ 70
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29
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 14 hours ago by • 0
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2
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More regions in union when increasing DBA$config$mergeOverlap
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1 day ago • updated 9 hours ago Ian D. ▴ 70
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2
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Deseq2 and Normalization of RNA sequencing data
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1 day ago • updated 1 hour ago kcarey • 0
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3
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93
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Differences in differential analysis methods for RNA-Seq
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updated 13 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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1
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98
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
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updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
3
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News: Bioconductor 3.19 is Released!
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1 day ago shepherl 3.9k
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Empty table plot using plotGseaTable()
fgsea
1 day ago Chris • 0
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3
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109
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Store output of matchPWM()
biostrings Biostrings
updated 1 day ago by 65k • written 1 day ago by ▴ 70
0
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3
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217
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log2FoldChange value is way too different when compared with counts(dds)
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updated 1 day ago by 41k • written 2 days ago by • 0
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192
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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1 day ago • updated 23 hours ago Yveto • 0
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6
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sgseq rnaseq
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204
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Help with error using camera() in limma
CAMERA limma
2 days ago Chris • 0
1
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1
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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
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1
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75
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Timecourse RNASeq analysis
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0
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1
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86
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
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News: BioC2024 deadlines approaching
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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
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1
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85
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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
2
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2
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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
0
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3
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208
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updated 2 days ago by 65k • written 3 days ago by • 0
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0
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55
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago Chris • 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)
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updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
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1
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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
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updated 6 days ago by 41k • written 7 days ago by • 0
1
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3
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Deseq2. decontXcounts not integers. Useful alternative?
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114
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ATACseq merge peaks
DiffBind
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1
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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
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7
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago pl23 • 0
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9
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342
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
7 days ago glaciya2018 • 0
1
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2
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141
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8 days ago • updated 7 days ago ATpoint ★ 4.1k
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131
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
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updated 8 days ago by 41k • written 8 days ago by • 0
0
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0
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how to do Differential splicing from SGSeq analysis
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8 days ago • updated 3 days ago Sara • 0
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240
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get BM error
ensembldb
updated 8 days ago by 65k • written 8 days ago by • 0
2
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5
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215
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 7 days ago by 65k • written 9 days ago by • 0
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago Dario Strbenac ★ 1.5k
1
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3
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202
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updated 8 days ago by 41k • written 8 days ago by ▴ 20
1
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4
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301
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DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
3
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297
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 40
1
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1
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161
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Citation for edgeR user guide
edgeR
updated 9 days ago by 50k • written 9 days ago by ▴ 30
0
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7
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687
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News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
9 weeks ago • updated 9 days ago shepherl 3.9k
45,611 results • Page 1 of 913
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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