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The difference when using Limma compare between 3 conditions vs 2 conditions
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5 weeks ago • updated 3 days ago Chris • 0
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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 3 days ago by • 0 • written 4.6 years ago by ▴ 10
14
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Why p value inconsistent when using different number of pathway score?
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13 days ago • updated 2 days ago Chris • 0
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
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updated 1 day ago by 65k • written 2.3 years ago by • 0
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SGSeq: moving toward diffex from SGSeq analysis
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updated 3 days ago by ▴ 200 • written 6.7 years ago by ▴ 80
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126
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Once again a "Model matrix not full rank"
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updated 15 hours ago by 65k • written 1 day ago by ▴ 130
0
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4
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239
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Minfi - estimatecellscount
min minfi
updated 4 days ago by 65k • written 5 weeks ago by • 0
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184
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Help with error using camera() in limma
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3 days ago Chris • 0
1
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4
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DEseq2 coefficient
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10 weeks ago • updated 2 days ago JKim • 0
0
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3
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109
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Differences in differential analysis methods for RNA-Seq
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updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
0
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3
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157
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 3 days ago by ★ 1.9k • written 15 days ago by • 0
0
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3
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219
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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 3 days ago by 65k • written 4 days ago by • 0
3
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3
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202
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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updated 4 days ago by ★ 4.1k • written 5 days ago by ▴ 10
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3
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 3 days ago by • 0 • written 13.0 years ago by ▴ 10
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3
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Store output of matchPWM()
biostrings Biostrings
updated 2 days ago by 65k • written 2 days ago by ▴ 70
0
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3
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229
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
2
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2
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1.1k
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limma for gene expression analysis with big and unbalanced sample size
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updated 3 days ago by • 0 • written 7.9 years ago by • 0
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104
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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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2
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DESeq2 v1.35.0
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updated 1 day ago by 41k • written 1 day ago by • 0
0
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2
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103
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Timecourse RNASeq analysis
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3 days ago • updated 18 hours ago Aurora • 0
0
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2
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204
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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3 days ago • updated 2 days ago Yveto • 0
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2
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DiffBind
2 days ago • updated 1 day ago Ian D. ▴ 70
2
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2
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174
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
4 days ago Chris • 0
1
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2
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159
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 3 hours ago by 50k • written 7 hours ago by • 0
2
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RNA-seq DESeq2
updated 9 hours ago by 41k • written 9 hours ago by • 0
1
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2
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271
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 7 hours ago Kim • 0
0
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2
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152
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 days ago by • 0
0
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1
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74
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
0
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1
reply
92
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putting my own expression data in deseq2
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updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
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68
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Version 3.15 S4Vectors packages are missing
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updated 3 days ago by 3.9k • written 3 days ago by • 0
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90
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Padj "NA" with thousands of low count although the raw read counts are quite large
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updated 3 days ago by 41k • written 4 days ago by • 0
1
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1
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91
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
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1
reply
212
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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 3 days ago by 65k • written 4 days ago by • 0
0
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1
reply
114
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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 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
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1
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39
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
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0
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1
reply
71
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Gene-by-sample covariates in limma
Metabolomics limma
updated 1 day ago by 50k • written 1 day ago by • 0
0
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1
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165
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 1 day ago by ▴ 10
0
votes
1
reply
32
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package goseq seems to be not available on the latest version of R
goseq
updated 4 hours ago by 50k • written 8 hours ago by • 0
0
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0
replies
62
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
4 days ago Chris • 0
0
votes
0
replies
98
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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
8 days ago • updated 19 hours ago glaciya2018 • 0
0
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0
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33
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
1 day ago yvonneh • 0
0
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0
replies
26
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago Ian D. ▴ 70
0
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0
replies
22
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dba.plotProfile() plotting and interpretation
DiffBind
11 hours ago Henry ▴ 10
0
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0
replies
24
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Handling multiple differential expression comparisons
DESeq2
10 hours ago Zainab • 0
3
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0
replies
47
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News: Bioconductor 3.19 is Released!
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2 days ago shepherl 3.9k
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0
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3 days ago Maria Doyle ▴ 70
0
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0
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67
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Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 7 hours ago Chris • 0
0
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0
replies
77
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
9 days ago • updated 4 days ago Sara • 0
0
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0
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flowStats for CyTOF
flowStats
1 day ago tholmes • 0
49 results • Page 1 of 1
Recent ...
Replies
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!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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