0
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1
reply
183
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
1
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2
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285
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 days ago • updated 10 days ago Dylan.Sheerin • 0
0
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0
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87
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Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
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10 days ago neilzhao ▴ 30
0
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1
reply
115
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
2
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7
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417
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deseq2 results
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12 days ago • updated 9 days ago sajadahmad41454 • 0
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78
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Treeio as.treedata function seq lenght error
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12 days ago nromerov • 0
2
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2
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286
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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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13 days ago • updated 7 days ago zzrammal • 0
3
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10
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487
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 13 days ago by • 0
2
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1
reply
186
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 65k • written 13 days ago by • 0
0
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1
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119
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Recovering my account credentials on Bioconductor
Bioconductor
updated 13 days ago by 3.9k • written 13 days ago by • 0
0
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0
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99
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
13 days ago Dinesh • 0
3
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5
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305
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Help with running egsea()
EGSEA
14 days ago • updated 12 days ago Chris ▴ 10
3
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1
reply
153
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How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
4
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5
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338
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
14 days ago • updated 5 days ago Chris ▴ 10
0
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3
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234
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Couldn't connect to server while using "pathways"
graphite
updated 14 days ago by 42k • written 14 days ago by • 0
2
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1
reply
148
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by 42k • written 14 days ago by ▴ 70
1
vote
1
reply
193
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Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by 42k • written 17 days ago by ▴ 10
2
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2
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233
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fgsea significant result
fgsea
15 days ago Chris ▴ 10
0
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44
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3.2k
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 6 days ago by 42k • written 15 months ago by • 0
0
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6
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306
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Once again a "Model matrix not full rank"
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updated 16 days ago by ★ 1.4k • written 18 days ago by ▴ 130
1
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2
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409
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 16 days ago by 50k • written 16 days ago by • 0
2
votes
3
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279
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package goseq seems to be not available on the latest version of R
goseq
updated 14 days ago by 50k • written 17 days ago by ▴ 20
2
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3
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258
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Too many significant genes when integrating gtex and tcga
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updated 15 days ago by ★ 4.1k • written 17 days ago by • 0
0
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0
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124
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dba.plotProfile() plotting and interpretation
DiffBind
17 days ago Henry ▴ 10
0
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1
reply
180
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 17 days ago by 50k • written 18 days ago by • 0
0
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1
reply
163
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Gene-by-sample covariates in limma
Metabolomics limma
updated 17 days ago by 50k • written 18 days ago by • 0
4
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2
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634
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 days ago • updated 14 days ago gene_bioconductor ▴ 10
0
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0
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100
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flowStats for CyTOF
flowStats
18 days ago tholmes • 0
0
votes
2
replies
175
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DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
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0
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95
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
18 days ago yvonneh • 0
0
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0
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89
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago Ian D. ▴ 70
0
votes
1
reply
142
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 18 days ago by • 0
0
votes
4
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379
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 8 days ago by • 0 • written 19 days ago by ▴ 70
0
votes
2
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215
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Deseq2 and Normalization of RNA sequencing data
DESeq2
18 days ago • updated 17 days ago kcarey • 0
0
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3
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228
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
1
vote
3
replies
306
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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 12 days ago by ★ 4.1k • written 19 days ago by • 0
4
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0
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145
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
19 days ago shepherl 3.9k
0
votes
0
replies
142
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Empty table plot using plotGseaTable()
fgsea
19 days ago • updated 17 days ago Chris ▴ 10
0
votes
3
replies
304
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
19 days ago • updated 18 days ago Yveto • 0
0
votes
1
reply
266
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 20 days ago by 65k • written 20 days ago by • 0
3
votes
4
replies
266
views
Help with error using camera() in limma
CAMERA limma
20 days ago Chris ▴ 10
1
vote
1
reply
158
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
20 days ago • updated 17 days ago Aurora • 0
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
0
votes
0
replies
96
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
20 days ago Maria Doyle ▴ 70
0
votes
1
reply
125
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 20 days ago by 3.9k • written 20 days ago by • 0
0
votes
1
reply
138
views
putting my own expression data in deseq2
DESeq2
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
2
votes
2
replies
238
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago Chris ▴ 10
0
votes
3
replies
282
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 65k • written 21 days ago by • 0
45,679 results • Page 2 of 914
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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