Showing : spia • reset
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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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1
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2.6k
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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
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2
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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
1
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2
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(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
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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
1
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2
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1.9k
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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
0
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0
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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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1
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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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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
5
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2
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1.5k
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SPIA::spia function output
SPIA
updated 7.3 years ago by ▴ 570 • written 7.3 years ago by ▴ 10
0
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1
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1.5k
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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
1.4k
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makeSPIAdata
SPIA SPIA
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 10
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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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2
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1.4k
views
question on SPIA pavkage application
Organism SPIA Organism SPIA
updated 12.7 years ago by ▴ 150 • written 12.7 years ago by ▴ 380
0
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0
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1.4k
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SPIA: inferring inhibited pathways from up-regulated genes?
Pathways SPIA Pathways SPIA
14.4 years ago Tarca, Adi ▴ 570
0
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4
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1.4k
views
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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0
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1.4k
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SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.4 years ago Tarca, Adi ▴ 570
0
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2
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1.3k
views
SPIA package
PROcess SPIA PROcess SPIA
12.7 years ago Jing Huang ▴ 380
0
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1
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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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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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1.2k
views
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
0
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1
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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
0
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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
0
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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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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
0
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0
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1.2k
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a possible bug in spia function
SPIA
6.8 years ago slava.ilyntskyy • 0
0
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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
0
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0
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1.2k
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Background for test in SPIA package.
Annotation Pathways SPIA Annotation Pathways SPIA
11.1 years ago Ian Sudbery ▴ 30
0
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1
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1.2k
views
SPIA package
graph SPIA graph SPIA
updated 14.1 years ago by ★ 7.4k • written 14.2 years ago by ▴ 200
1
vote
1
reply
1.2k
views
SPIA plotP giving error
SPIA plotP threshold
7.5 years ago docpriya21 ▴ 10
0
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1
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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
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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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1.1k
views
question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
12.7 years ago Tarca, Adi ▴ 570
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
0
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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
0
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0
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1.0k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
14.0 years ago January Weiner ▴ 370
0
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0
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1.0k
views
SPIA error in DE-Colorectal
SPIA
7.9 years ago saamar.rajput • 0
0
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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
0
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0
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993
views
Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
13.4 years ago Tarca, Adi ▴ 570
0
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0
replies
977
views
How to create KEGG's pathway data for SPIA?
SPIA SPIA
13.5 years ago Lourdes Peña Castillo ▴ 140
0
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0
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947
views
help with SPIA package
Organism limma SPIA Organism limma SPIA
14.0 years ago Barbara Bo-Ju Shih ▴ 40
0
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0
replies
936
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
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1
reply
856
views
alternative package to SPIA
SPIA pathway enrichment analysis overrepresentation
5.2 years ago asifgeb • 0
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0
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855
views
MArray into data.frame for SPIA package
limma marray SPIA limma marray SPIA
14.1 years ago Gordon Smyth 50k
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0
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782
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
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
46 results • Page 1 of 1
Recent ...
Replies
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
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)`)?
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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
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