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The difference when using Limma compare between 3 conditions vs 2 conditions
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Why p value inconsistent when using different number of pathway score?
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updated 14 hours ago by • 0 • written 6.7 years ago by ▴ 80
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 4 days ago by 65k • written 2.3 years ago by • 0
4
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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4 days ago • updated 5 hours ago gene_bioconductor ▴ 10
3
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Method to find pathways different between 2 groups
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Help with running egsea()
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3 hours ago • updated 1 hour ago Chris • 0
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Help with error using camera() in limma
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fgsea significant result
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1 day ago Chris • 0
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limma for gene expression analysis with big and unbalanced sample size
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updated 6 days ago by • 0 • written 7.9 years ago by • 0
2
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package goseq seems to be not available on the latest version of R
goseq
updated 11 hours ago by 50k • written 3 days ago by ▴ 20
2
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Too many significant genes when integrating gtex and tcga
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updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
2
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1
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39
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How to save the DEXSeq results
DEXSeq
updated 8 hours ago by 41k • written 8 hours ago by • 0
1
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3
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71
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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1
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1
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109
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
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2
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 3 days ago Kim • 0
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 2 days ago by 50k • written 3 days ago by • 0
1
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1
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99
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Handling multiple differential expression comparisons
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updated 1 day ago by 41k • written 3 days ago by ▴ 10
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2
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Improving the design matrices vignette in RNAseq123
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Trim/Filter out-of-bounds GRanges
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updated 8 hours ago by 41k • written 9 hours ago by ▴ 70
1
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6 weeks ago • updated 4 hours ago shepherl 3.9k
1
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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5 days ago • updated 4 days ago Yveto • 0
1
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4
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DEseq2 coefficient
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10 weeks ago • updated 5 days ago JKim • 0
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Empty table plot using plotGseaTable()
fgsea
5 days ago • updated 3 days ago Chris • 0
0
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6
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212
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Once again a "Model matrix not full rank"
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updated 2 days ago by ★ 1.3k • written 4 days ago by ▴ 130
0
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5
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DNAString: Standard checksum function?
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8.2 years ago • updated 1 day ago Henrik Bengtsson ★ 2.4k
0
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3
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Couldn't connect to server while using "pathways"
graphite
updated 3 hours ago by 41k • written 16 hours ago by • 0
0
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3
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[Mfuzz] Error in cmeans(exprs(eset)
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updated 3 hours ago by • 0 • written 13.1 years ago by ▴ 720
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34
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
15 months ago • updated 1 hour ago Poonam • 0
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need help with Diffbind multiple groups
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31 minutes ago • updated 30 minutes ago Dinesh • 0
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flowStats for CyTOF
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4 days ago tholmes • 0
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S4Vectors
updated 6 days ago by 3.9k • written 6 days ago by • 0
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News: BioC2024 deadlines approaching
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6 days ago Maria Doyle ▴ 70
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103
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
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3
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167
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by ★ 1.9k • written 18 days ago by • 0
0
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3
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242
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
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updated 6 days ago by 65k • written 7 days ago by • 0
0
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1
reply
228
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
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updated 6 days ago by 65k • written 6 days ago by • 0
0
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3
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Limma, eBayes different sample size of groups and adjustment
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updated 6 days ago by • 0 • written 13.0 years ago by ▴ 10
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3
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156
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Store output of matchPWM()
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updated 5 days ago by 65k • written 5 days ago by ▴ 70
0
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1
reply
142
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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 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
3
replies
251
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
2
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166
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limma-voom: Calculate the log-fold change in gene expression within a sample
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written 13 days ago by • 0
0
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3
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135
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Differences in differential analysis methods for RNA-Seq
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updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
0
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1
reply
68
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 4 days ago by • 0
0
votes
2
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131
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
5 days ago • updated 4 days ago Ian D. ▴ 70
0
votes
0
replies
43
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 days ago Ian D. ▴ 70
0
votes
0
replies
48
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
4 days ago yvonneh • 0
0
votes
2
replies
107
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DESeq2 v1.35.0
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updated 4 days ago by 41k • written 4 days ago by • 0
57 results • Page 1 of 2
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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