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The difference when using Limma compare between 3 conditions vs 2 conditions
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5 weeks ago • updated 4 days ago Chris • 0
14
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Why p value inconsistent when using different number of pathway score?
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14 days ago • updated 3 days ago Chris • 0
8
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by ▴ 200 • written 6.7 years ago by ▴ 80
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19
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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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updated 4 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 2 days ago by 65k • written 2.3 years ago by • 0
3
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4
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191
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Help with error using camera() in limma
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4 days ago Chris • 0
3
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0
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55
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News: Bioconductor 3.19 is Released!
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3 days ago shepherl 3.9k
3
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3
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 5 days ago by ★ 4.1k • written 5 days ago by ▴ 10
2
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2
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105
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
2
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2
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updated 4 days ago by • 0 • written 7.9 years ago by • 0
2
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178
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
5 days ago Chris • 0
1
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2
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282
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 23 hours ago Kim • 0
1
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4
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474
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DEseq2 coefficient
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10 weeks ago • updated 3 days ago JKim • 0
1
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1
reply
94
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
1
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2
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296
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 19 hours ago by 50k • written 23 hours ago by • 0
1
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1
reply
180
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 2 days ago by ▴ 10
0
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3
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112
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
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1
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43
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by • 0
0
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2
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111
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago Ian D. ▴ 70
0
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0
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31
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DiffBind
2 days ago Ian D. ▴ 70
0
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0
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38
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
2 days ago yvonneh • 0
0
votes
2
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78
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DESeq2 v1.35.0
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updated 2 days ago by 41k • written 2 days ago by • 0
0
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0
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31
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flowStats for CyTOF
flowStats
2 days ago tholmes • 0
0
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1
reply
81
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Gene-by-sample covariates in limma
Metabolomics limma
updated 1 day ago by 50k • written 2 days ago by • 0
0
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1
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85
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 2 days ago by • 0
0
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2
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112
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Deseq2 and Normalization of RNA sequencing data
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2 days ago • updated 1 day ago kcarey • 0
0
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0
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110
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
9 days ago • updated 1 day ago glaciya2018 • 0
0
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2
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109
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Timecourse RNASeq analysis
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4 days ago • updated 1 day ago Aurora • 0
0
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0
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33
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dba.plotProfile() plotting and interpretation
DiffBind
1 day ago Henry ▴ 10
0
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0
replies
37
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Handling multiple differential expression comparisons
DESeq2
1 day ago Zainab • 0
0
votes
0
replies
72
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Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 23 hours ago Chris • 0
0
votes
1
reply
56
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package goseq seems to be not available on the latest version of R
goseq
updated 20 hours ago by 50k • written 1 day ago by • 0
0
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0
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79
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how to do Differential splicing from SGSeq analysis
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10 days ago • updated 5 days ago Sara • 0
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6
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164
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Once again a "Model matrix not full rank"
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updated 14 hours ago by ★ 1.3k • written 1 day ago by ▴ 130
0
votes
4
replies
241
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Minfi - estimatecellscount
min minfi
updated 5 days ago by 65k • written 5 weeks ago by • 0
0
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0
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64
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago Chris • 0
0
votes
1
reply
94
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putting my own expression data in deseq2
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
1
reply
72
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 4 days ago by 3.9k • written 4 days ago by • 0
0
votes
0
replies
54
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News: BioC2024 deadlines approaching
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4 days ago Maria Doyle ▴ 70
0
votes
1
reply
93
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
3
replies
158
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by ★ 1.9k • written 16 days ago by • 0
0
votes
3
replies
225
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 4 days ago by 65k • written 5 days ago by • 0
0
votes
1
reply
215
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 4 days ago by 65k • written 4 days ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
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updated 4 days ago by • 0 • written 13.0 years ago by ▴ 10
0
votes
3
replies
139
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Store output of matchPWM()
biostrings Biostrings
updated 3 days ago by 65k • written 3 days ago by ▴ 70
0
votes
1
reply
121
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
3
replies
233
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
2
replies
210
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
3 days ago • updated 2 days ago Yveto • 0
0
votes
2
replies
155
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 days ago by • 0
49 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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