1
vote
2
replies
290
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 18 hours ago by 50k • written 21 hours ago by • 0
0
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1
reply
56
views
package goseq seems to be not available on the latest version of R
goseq
updated 19 hours ago by 50k • written 22 hours ago by • 0
2
votes
2
replies
103
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 23 hours ago by 41k • written 23 hours ago by • 0
0
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0
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35
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Handling multiple differential expression comparisons
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1 day ago Zainab • 0
0
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0
replies
33
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dba.plotProfile() plotting and interpretation
DiffBind
1 day ago Henry ▴ 10
0
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6
replies
159
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Once again a "Model matrix not full rank"
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updated 12 hours ago by ★ 1.3k • written 1 day ago by ▴ 130
0
votes
1
reply
172
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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
84
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 2 days ago by • 0
0
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1
reply
79
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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
votes
0
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31
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flowStats for CyTOF
flowStats
2 days ago tholmes • 0
0
votes
2
replies
78
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DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
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0
replies
38
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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
31
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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
43
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by • 0
0
votes
2
replies
111
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Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
votes
3
replies
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
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
3
votes
0
replies
55
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
2 days ago shepherl 3.9k
0
votes
0
replies
72
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Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 21 hours ago Chris • 0
0
votes
3
replies
139
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Store output of matchPWM()
biostrings Biostrings
updated 2 days ago by 65k • written 3 days ago by ▴ 70
0
votes
2
replies
109
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
209
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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
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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
0
votes
0
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54
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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
replies
109
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Timecourse RNASeq analysis
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4 days ago • updated 1 day ago Aurora • 0
0
votes
1
reply
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 4 days ago by 65k • written 4 days ago by • 0
0
votes
1
reply
93
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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
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 • updated 4 days ago Chris • 0
0
votes
0
replies
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
3
replies
225
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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
1
vote
1
reply
114
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 7 days ago by ▴ 40 • written 8 days ago by ★ 1.5k
1
vote
3
replies
203
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 8 days ago by 41k • written 8 days ago by • 0
1
vote
7
replies
307
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago pl23 • 0
2
votes
9
replies
363
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 9 days ago by • 0
0
votes
0
replies
109
views
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
2
replies
193
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PCA plot suggestions
DESeq2 PCAtools
updated 8 days ago by 41k • written 9 days ago by • 0
0
votes
1
reply
143
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
127
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ATACseq merge peaks
DiffBind
updated 8 days ago by ★ 4.1k • written 10 days ago by • 0
0
votes
0
replies
79
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 days ago • updated 5 days ago Sara • 0
0
votes
0
replies
79
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago Dario Strbenac ★ 1.5k
1
vote
2
replies
152
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
10 days ago • updated 9 days ago ATpoint ★ 4.1k
1
vote
3
replies
205
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 20
1
vote
4
replies
313
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago winwater0928 • 0
2
votes
5
replies
253
views
get BM error
ensembldb
updated 10 days ago by 65k • written 10 days ago by • 0
2
votes
5
replies
229
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 9 days ago by 65k • written 10 days ago by • 0
200 results • Page 1 of 4
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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