Showing : mroast • reset
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
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
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
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
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
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
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
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
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
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
1
reply
1.5k
views
Graphic representation of mroast results
mroast visualization
8.9 years ago Elena Serrano ▴ 30
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
3
replies
1.4k
views
ROAST using curated gene sets
edgeR mroast roast
7.9 years ago lattalic • 0
4
votes
4
replies
1.4k
views
Interpreting mroast results
mroast limma roast
5.4 years ago SB • 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
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
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
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
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
3
votes
4
replies
835
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
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
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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