1
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2
replies
283
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 hours ago by 50k • written 20 hours ago by • 0
0
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1
reply
55
views
package goseq seems to be not available on the latest version of R
goseq
updated 18 hours ago by 50k • written 21 hours ago by • 0
2
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2
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102
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 22 hours ago by 41k • written 22 hours ago by • 0
0
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0
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34
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Handling multiple differential expression comparisons
DESeq2
23 hours ago Zainab • 0
0
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0
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32
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dba.plotProfile() plotting and interpretation
DiffBind
1 day ago Henry ▴ 10
0
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6
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158
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Once again a "Model matrix not full rank"
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updated 11 hours ago by ★ 1.3k • written 1 day ago by ▴ 130
0
votes
1
reply
171
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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
83
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
1
reply
78
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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
votes
0
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30
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flowStats for CyTOF
flowStats
2 days ago tholmes • 0
0
votes
2
replies
77
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
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0
replies
37
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
2 days ago yvonneh • 0
0
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0
replies
30
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago Ian D. ▴ 70
0
votes
1
reply
41
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by • 0
0
votes
2
replies
110
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
votes
3
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111
views
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
votes
1
reply
120
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
3
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0
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53
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
2 days ago shepherl 3.9k
0
votes
0
replies
71
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Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 20 hours ago Chris • 0
0
votes
3
replies
138
views
Store output of matchPWM()
biostrings Biostrings
updated 2 days ago by 65k • written 3 days ago by ▴ 70
0
votes
2
replies
108
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago Ian D. ▴ 70
0
votes
2
replies
208
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
3
replies
233
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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
3
votes
4
replies
190
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Help with error using camera() in limma
CAMERA limma
4 days ago • updated 3 days ago Chris • 0
1
vote
1
reply
94
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
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0
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53
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News: BioC2024 deadlines approaching
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4 days ago Maria Doyle ▴ 70
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
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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1
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71
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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
1
reply
215
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 3 days ago by 65k • written 4 days ago by • 0
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 4 days ago by • 0
2
votes
2
replies
177
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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
0
votes
0
replies
64
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago Chris • 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
3
votes
3
replies
207
views
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
0
votes
0
replies
109
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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
votes
0
replies
79
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 days ago • updated 5 days ago Sara • 0
0
votes
2
replies
155
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limma-voom: Calculate the log-fold change in gene expression within a sample
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written 11 days ago by • 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 2 days ago Chris • 0
0
votes
3
replies
157
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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
1
vote
2
replies
279
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 21 hours ago Kim • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 4 days ago Chris • 0
0
votes
4
replies
240
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Minfi - estimatecellscount
min minfi
updated 5 days ago by 65k • written 5 weeks ago by • 0
1
vote
4
replies
474
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 2 days ago JKim • 0
5
votes
6
replies
2.8k
views
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
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by • 0 • written 4.6 years ago by ▴ 10
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by ▴ 200 • written 6.7 years ago by ▴ 80
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 3 days ago by • 0 • written 7.9 years ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 3 days ago by • 0 • written 13.0 years ago by ▴ 10
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: 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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