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4
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deseq2 results
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Treeio as.treedata function seq lenght error
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
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Extremely small p-values using Limma for proteomic data
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minfi latest update for EPIC V2 chip
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Recovering my account credentials on Bioconductor
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need help with Diffbind multiple groups
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1 day ago Dinesh • 0
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Help with running egsea()
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6 weeks ago • updated 1 day ago shepherl 3.9k
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How to save the DEXSeq results
DEXSeq
updated 1 day ago by 42k • written 1 day ago by • 0
3
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Method to find pathways different between 2 groups
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updated 9 hours ago by 50k • written 2 days ago by • 0
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3
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graphite
updated 1 day ago by 42k • written 2 days ago by • 0
1
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79
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 1 day ago by 42k • written 1 day ago by ▴ 70
1
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3
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233
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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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updated 1 day ago by 16k • written 2 days ago by • 0
1
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109
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Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by 42k • written 4 days ago by ▴ 10
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fgsea significant result
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3 days ago • updated 2 days ago Chris • 0
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
15 months ago • updated 1 day ago Poonam • 0
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Once again a "Model matrix not full rank"
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updated 4 days ago by ★ 1.3k • written 5 days ago by ▴ 130
1
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2
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338
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 4 days ago by 50k • written 4 days ago by • 0
2
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package goseq seems to be not available on the latest version of R
goseq
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2
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 5 days ago by 50k • written 5 days ago by • 0
0
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updated 5 days ago by 50k • written 5 days 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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5 days ago • updated 1 day ago gene_bioconductor ▴ 10
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flowStats for CyTOF
flowStats
5 days ago tholmes • 0
0
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2
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113
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updated 5 days ago by 42k • written 5 days ago by • 0
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DiffBind: no peaks in DBA object
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5 days ago yvonneh • 0
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5 days ago Ian D. ▴ 70
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1
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77
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 5 days ago by • 0
0
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2
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 days ago • updated 5 days ago Ian D. ▴ 70
0
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Deseq2 and Normalization of RNA sequencing data
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6 days ago • updated 5 days ago kcarey • 0
0
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updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
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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 23 minutes ago by ★ 4.1k • written 6 days ago by • 0
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Empty table plot using plotGseaTable()
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6 days ago • updated 4 days ago Chris • 0
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Store output of matchPWM()
biostrings Biostrings
updated 6 days ago by 65k • written 6 days ago by ▴ 70
0
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3
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log2FoldChange value is way too different when compared with counts(dds)
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updated 6 days ago by 42k • written 7 days ago by • 0
1
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2
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239
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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7 days ago • updated 6 days ago Yveto • 0
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SGSeq: moving toward diffex from SGSeq analysis
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updated 1 day ago by • 0 • written 6.7 years ago by ▴ 80
0
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232
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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 7 days ago by 65k • written 8 days ago by • 0
3
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4
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Help with error using camera() in limma
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7 days ago Chris • 0
1
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1
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119
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
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2
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Timecourse RNASeq analysis
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8 days ago • updated 4 days ago Aurora • 0
0
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1
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109
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by 42k • written 8 days ago by • 0
0
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0
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News: BioC2024 deadlines approaching
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93
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 7 days ago by 3.9k • written 8 days ago by • 0
0
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1
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113
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putting my own expression data in deseq2
DESeq2
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
2
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2
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204
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
8 days ago Chris • 0
0
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3
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246
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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 7 days ago by 65k • written 8 days ago by • 0
45,630 results • Page 1 of 913
Recent ...
Replies
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Ask yourself the question how a gene that is exactly the same everywhere adds anything to any analysis. Heatmaps usually take DEGs to infer…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
I'd argue that most users, especially the general reader of a paper is interested in a visual representation of the data **and** applied cu…
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
I'd also add that plotting adjusted P-values in the y-axis of the volcano plot is not the recommended way to produce a volcano plot. This h…
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Votes
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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