Showing : mroast • reset
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma mroast GSEA GO illumina human ht-12 v4
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
6
votes
10
replies
1.8k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
9.0 years ago svlachavas ▴ 830
7
votes
10
replies
1.7k
views
Possible TF binding site enrichment analysis through mroast and conversion problems
TF binding site analysis bioconductor mroast limma promoter analysis
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
7
votes
9
replies
3.0k
views
limma's mroast and romer
romer mroast limma
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 10
7
votes
6
replies
3.2k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma mroast barcodeplot KEGG gene set testing
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 830
0
votes
6
replies
1.8k
views
Different results obtained from mroast and camera from Deseq2 counts
limma camera mroast tximport
updated 6.8 years ago by 65k • written 6.9 years ago by ▴ 40
2
votes
6
replies
1.6k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
9.1 years ago svlachavas ▴ 830
4
votes
4
replies
1.4k
views
Interpreting mroast results
mroast limma roast
5.4 years ago SB • 0
8
votes
4
replies
5.6k
views
Differences between edgeR's and limma+voom's implementation of camera/roast/romer
limma edger mroast romer camera
updated 8.2 years ago by ★ 13k • written 8.2 years ago by ▴ 180
3
votes
4
replies
834
views
Is number of rotations dependent on number of gene sets in mroast?
limma mroast
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
0
votes
4
replies
1.6k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 9.1 years ago by ★ 1.6k • written 9.1 years ago by ▴ 830
0
votes
3
replies
1.9k
views
Barcodeplot limma function using two logFC lists
limma edger barcodeplot gene set enrichment mroast
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
2
votes
3
replies
1.4k
views
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma agilent microarrays mroast fry gene tests gene set testing
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
0
votes
3
replies
1.4k
views
ROAST using curated gene sets
edgeR mroast roast
7.9 years ago lattalic • 0
3
votes
3
replies
921
views
Conditions for using Fry
limma mroast fry
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
2
votes
2
replies
1.3k
views
limma roast/mroast with patient-matched pre-/post- treatment
limma roast mroast block
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by • 0
2
votes
2
replies
1.2k
views
Running Roast with Gene Symbols of Curated Genes
mroast roast gene set gene set analysis edgeR
updated 7.9 years ago by 65k • written 7.9 years ago by • 0
0
votes
2
replies
1.5k
views
using camera/roast/romer to find enriched gene sets from proteomics data
limma proteomics camera mroast romer
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
0
votes
2
replies
918
views
mroast/fry with gene weights for most or all genes
limma mroast fry
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 180
1
vote
2
replies
1.3k
views
Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
limma mroast agilent microarrays GO.BP barcodeplot
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 830
0
votes
1
reply
1.5k
views
Graphic representation of mroast results
mroast visualization
8.9 years ago Elena Serrano ▴ 30
0
votes
0
replies
624
views
Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast camera gene set testing
3.6 years ago svlachavas ▴ 830
22 results • Page 1 of 1
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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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