Showing : spia • reset
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SPIA - changes between 1.4.0 and 1.60.
Pathways SPIA Pathways SPIA
updated 13.7 years ago by ▴ 20 • written 13.7 years ago by ▴ 480
0
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3
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2.7k
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Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 11.9 years ago by ▴ 120 • written 11.9 years ago by ▴ 50
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2
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1.4k
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question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.7 years ago by ▴ 150 • written 12.7 years ago by ▴ 380
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2
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1.3k
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SPIA package
PROcess SPIA PROcess SPIA
12.7 years ago Jing Huang ▴ 380
1
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2
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383
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Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
SPIA
6 months ago Benji Bromberg ▴ 20
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2
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1.6k
views
organism abbreviations (SPIA package)
Microarray Organism SPIA Microarray Organism SPIA
updated 12.7 years ago by ▴ 340 • written 12.7 years ago by ▴ 380
1
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2
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1.9k
views
Question on graphite/SPIA; extracting DE gene list
graphite spia runSPIA
updated 5.3 years ago by 0 • written 9.2 years ago by • 0
1
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2
replies
2.4k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
8.8 years ago svlachavas ▴ 830
5
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2
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1.5k
views
SPIA::spia function output
SPIA
updated 7.3 years ago by ▴ 570 • written 7.3 years ago by ▴ 10
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2
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2.4k
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Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!
Organism limma SPIA Organism limma SPIA
updated 12.3 years ago by ▴ 570 • written 12.3 years ago by ▴ 100
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1
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2.1k
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SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 21 months ago by • 0 • written 9.5 years ago by • 0
0
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1
reply
1.5k
views
Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 13.2 years ago by ▴ 370 • written 13.2 years ago by ▴ 100
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1
reply
856
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
0
votes
1
reply
1.2k
views
SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 13.4 years ago by ★ 7.2k • written 13.4 years ago by ▴ 20
1
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1
reply
1.2k
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SPIA plotP giving error
SPIA plotP threshold
7.5 years ago docpriya21 ▴ 10
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1
reply
1.1k
views
a question on SPIA package
Microarray SPIA Microarray SPIA
updated 12.7 years ago by ▴ 650 • written 12.7 years ago by ▴ 380
0
votes
1
reply
1.2k
views
SPIA package
graph SPIA graph SPIA
updated 14.1 years ago by ★ 7.4k • written 14.2 years ago by ▴ 200
0
votes
1
reply
1.2k
views
Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 13.2 years ago by ▴ 300 • written 13.2 years ago by ▴ 370
0
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1
reply
1.4k
views
makeSPIAdata
SPIA SPIA
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 10
0
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1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways SPIA cycle graphite Pathways SPIA cycle graphite
10.3 years ago array chip ▴ 420
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1
reply
1.3k
views
SPIA
Pathways SPIA Pathways SPIA
updated 10.2 years ago by ▴ 570 • written 10.2 years ago by ★ 13k
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1
reply
2.6k
views
SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive.
SPIA cycle SPIA cycle
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ★ 13k
0
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0
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936
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
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0
replies
782
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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1.2k
views
Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.1 years ago Ian Sudbery ▴ 30
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0
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1.4k
views
SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.4 years ago Tarca, Adi ▴ 570
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0
replies
855
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.1 years ago Gordon Smyth 50k
0
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0
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946
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help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
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0
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1.0k
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SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.0 years ago January Weiner ▴ 370
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0
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1.1k
views
SPIA with Mouse Data
Genetics Network Organism SPIA Genetics Network Organism SPIA
13.8 years ago Will Bush ▴ 10
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0
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977
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How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.5 years ago Lourdes Peña Castillo ▴ 140
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0
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1.3k
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Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.5 years ago Tarca, Adi ▴ 570
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0
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993
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Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.4 years ago Tarca, Adi ▴ 570
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0
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1.1k
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question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.7 years ago Tarca, Adi ▴ 570
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0
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1.2k
views
question for SPIA package
Pathways SPIA Pathways SPIA
12.4 years ago Jing Huang ▴ 380
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0
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1.4k
views
SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.4 years ago Tarca, Adi ▴ 570
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0
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1.2k
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Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
12.4 years ago January Weiner ▴ 240
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0
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1.0k
views
Overrepresentation pathway with KEGGPROFILE and SPIA
SPIA SPIA
11.3 years ago gregory voisin ▴ 430
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0
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1.2k
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Bioconductor Digest, Vol 119, Issue 5: Overrepresentation pathway with KEGGPROFILE and SPIA
Pathways SPIA KEGGprofile Pathways SPIA KEGGprofile
11.3 years ago Tarca, Adi ▴ 570
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0
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1.4k
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changes in SPIA package: using updated KEGG pathway data
Organism SPIA Organism SPIA
11.2 years ago Tarca, Adi ▴ 570
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0
replies
1.7k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.2 years ago Tarca, Adi ▴ 570
0
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0
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1.2k
views
SPIA, hacked to run with only selected pathways
SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA
14.4 years ago Tarca, Adi ▴ 570
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0
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1.0k
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R: Re: Deseq2 and differentia expression
SPIA SPIA
9.8 years ago Simon Anders ★ 3.7k
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1.0k
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SPIA error in DE-Colorectal
SPIA
7.9 years ago saamar.rajput • 0
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0
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1.1k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.9 years ago khhgng • 0
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0
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1.2k
views
a possible bug in spia function
SPIA
6.8 years ago slava.ilyntskyy • 0
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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