Showing : mroast • reset
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Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast camera gene set testing
2.7 years ago svlachavas ▴ 810
4
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4
replies
1.0k
views
Interpreting mroast results
mroast limma roast
4.5 years ago SB • 0
1
vote
2
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988
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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 4.6 years ago by 47k • written 4.6 years ago by ▴ 810
2
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3
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981
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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 4.6 years ago by 47k • written 4.7 years ago by ▴ 810
0
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2
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656
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mroast/fry with gene weights for most or all genes
limma mroast fry
updated 4.7 years ago by 47k • written 4.7 years ago by ▴ 160
3
votes
3
replies
607
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Conditions for using Fry
limma mroast fry
updated 4.8 years ago by 47k • written 4.8 years ago by • 0
3
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4
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562
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Is number of rotations dependent on number of gene sets in mroast?
limma mroast
updated 4.8 years ago by 47k • written 4.8 years ago by • 0
0
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3
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1.5k
views
Barcodeplot limma function using two logFC lists
limma edger barcodeplot gene set enrichment mroast
updated 5.4 years ago by 47k • written 5.4 years ago by • 0
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6
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1.4k
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Different results obtained from mroast and camera from Deseq2 counts
limma camera mroast tximport
updated 5.9 years ago by 63k • written 5.9 years ago by ▴ 40
0
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2
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1.2k
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using camera/roast/romer to find enriched gene sets from proteomics data
limma proteomics camera mroast romer
updated 6.7 years ago by 47k • written 6.7 years ago by • 0
2
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2
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1.0k
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limma roast/mroast with patient-matched pre-/post- treatment
limma roast mroast block
updated 6.9 years ago by 7.8k • written 6.9 years ago by • 0
2
votes
2
replies
893
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Running Roast with Gene Symbols of Curated Genes
mroast roast gene set gene set analysis edgeR
updated 7.0 years ago by 63k • written 7.0 years ago by • 0
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3
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1.1k
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ROAST using curated gene sets
edgeR mroast roast
7.0 years ago lattalic • 0
6
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4
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4.4k
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Differences between edgeR's and limma+voom's implementation of camera/roast/romer
limma edger mroast romer camera
updated 7.3 years ago by 13k • written 7.3 years ago by ▴ 160
7
votes
6
replies
2.8k
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 7.5 years ago by 47k • written 7.5 years ago by ▴ 810
7
votes
9
replies
2.5k
views
limma's mroast and romer
romer mroast limma
updated 7.7 years ago by 47k • written 7.7 years ago by ▴ 10
7
votes
10
replies
1.4k
views
Possible TF binding site enrichment analysis through mroast and conversion problems
TF binding site analysis bioconductor mroast limma promoter analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 810
5
votes
11
replies
1.5k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma mroast GSEA GO illumina human ht-12 v4
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 810
0
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1
reply
1.3k
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Graphic representation of mroast results
mroast visualization
8.0 years ago Elena Serrano ▴ 30
6
votes
10
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1.5k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
8.1 years ago • updated 8.0 years ago svlachavas ▴ 810
0
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4
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1.3k
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Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by ▴ 810
2
votes
6
replies
1.3k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
8.2 years ago svlachavas ▴ 810
22 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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Scholar to Mike Smith ★ 6.0k
Popular Question to Martin Morgan 25k
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Popular Question to Gordon Smyth 47k
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