15
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The difference when using Limma compare between 3 conditions vs 2 conditions
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4 weeks ago • updated 2 days ago Chris • 0
14
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12 days ago • updated 1 day ago Chris • 0
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updated 1 day ago by ▴ 200 • written 6.7 years ago by ▴ 80
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updated 2 days ago by • 0 • written 4.6 years ago by ▴ 10
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 9 hours ago by 65k • written 2.3 years ago by • 0
3
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
1 day ago shepherl 3.9k
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4
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Help with error using camera() in limma
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2 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)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
2
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2
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 2 days ago by • 0 • written 7.9 years ago by • 0
2
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169
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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
1
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7
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294
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago pl23 • 0
1
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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
1
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3
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187
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
1
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2
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695
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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15 days ago • updated 6 days ago ussarizona ▴ 10
1
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4
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301
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
1
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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
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
1
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4
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456
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DEseq2 coefficient
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9 weeks ago • updated 1 day ago JKim • 0
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2
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66
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Deseq2 and Normalization of RNA sequencing data
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1 day ago • updated 2 hours ago kcarey • 0
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3
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DEXSeq
updated 2 days ago by ★ 1.9k • written 14 days ago by • 0
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News: BioC2024 deadlines approaching
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2 days ago Maria Doyle ▴ 70
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63
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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
0
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3
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209
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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 2 days ago by 65k • written 3 days ago by • 0
0
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1
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204
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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 2 days ago by 65k • written 2 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 2 days ago by • 0 • written 13.0 years ago by ▴ 10
0
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1
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86
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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
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
0
votes
4
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237
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Minfi - estimatecellscount
min minfi
updated 3 days ago by 65k • written 4 weeks ago by • 0
0
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1
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103
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 22 minutes ago by 50k • written 6 hours ago by ▴ 10
0
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3
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110
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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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0
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72
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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
0
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2
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182
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PCA plot suggestions
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updated 6 days ago by 41k • written 7 days 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
0
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0
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55
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Empty table plot using plotGseaTable()
fgsea
1 day ago Chris • 0
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)
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
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2
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192
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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2 days ago • updated 1 day ago Yveto • 0
0
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2
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150
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limma-voom: Calculate the log-fold change in gene expression within a sample
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written 10 days ago by • 0
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 15 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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1
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29
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 hours ago by • 0
0
votes
2
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88
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 10 hours ago Ian D. ▴ 70
0
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0
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15
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
10 hours ago Ian D. ▴ 70
0
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0
replies
17
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
10 hours ago yvonneh • 0
0
votes
1
reply
114
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ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
0
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2
replies
48
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DESeq2 v1.35.0
DESeq2
updated 9 hours ago by 41k • written 9 hours ago by • 0
0
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0
replies
13
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flowStats for CyTOF
flowStats
8 hours ago tholmes • 0
0
votes
3
replies
53
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Once again a "Model matrix not full rank"
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4 hours ago arfranco ▴ 130
0
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1
reply
34
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Gene-by-sample covariates in limma
Metabolomics limma
updated 2 hours ago by 50k • written 7 hours ago by • 0
0
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1
reply
28
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 2 hours ago by 50k • written 7 hours ago by • 0
0
votes
1
reply
86
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
75
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
50 results • Page 1 of 1
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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