User: Tarca, Adi

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Tarca, Adi570
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2 years, 11 months ago
Joined:
14 years, 1 month ago
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a*****@med.wayne.edu

Posts by Tarca, Adi

<prev • 56 results • page 1 of 6 • next >
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Answer: A: SPIA::spia function output
... >Dear SPIA package maintainer, My name is Franklin Johnson. I think of myself as a data scientist, and I have no professional affiliation at this moment with regard to this post. I downloaded the 134 Malus domestica ('mdm') pathways using the KEGGREST package and successfully made the spia data ...
written 2.9 years ago by Tarca, Adi570
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Comment: C: summarizeOverlaps error with hg38
... Thanks Julian, this sounds like a good reason for the error.  ...
written 3.9 years ago by Tarca, Adi570
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summarizeOverlaps error with hg38
... Hi all, I try to use summarizeOverlaps function on a GRangesList and get the error below.      library(GenomicFeatures) library(GenomicRanges) library(Rsamtools) library(GenomicAlignments) library(TxDb.Hsapiens.UCSC.hg38.knownGene) txdb2 <- TxDb.Hsapiens.UCSC.hg38.knownGene ex=exonsBy(txd ...
summarizeoverlaps written 3.9 years ago by Tarca, Adi570 • updated 3.9 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: (Gene-set)Pathway analysis based on network/pathway topology in R
... Hi , Please see https://support.bioconductor.org/p/51142/ for some info on how to use R to download recent KEGG xml files for use with SPIA. Adi Tarca ...
written 4.4 years ago by Tarca, Adi570
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Comment: C: Question on graphite/SPIA; extracting DE gene list
... Hi Ramya,   prepareSPIA creates a R data file, "keggexSPIA.RData", in the current working directory and the file contains a list with all the  pathways to be tested. prepareSPIA(kegg, "keggex") You can load that file: load("keggexSPIA.RData") and see the vignette of SPIA how to extract informa ...
written 4.8 years ago by Tarca, Adi570
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Answer: A: UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
... Dear Herv?, I have seen that type of error in google search but usually was for one or few transcripts. Seeing that the problem was for maybe all of the transcripts, I was not sure that the table was properly downloaded. Thank you for the clarification and for making others aware of the issue. Best ...
written 5.6 years ago by Tarca, Adi570
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Answer: A: SPIA
... Hi Martin, Not all pathways end up being parsed and analyzed. There is a minimum number of connections that are needed to make any use of the topology. For instance if you look in the hsa03030.xml file you will see no relation (edge) between any node, as opposed to another random pathway (hsa05330) ...
written 5.8 years ago by Tarca, Adi570
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Answer: A: makeSPIAdata
... Hi Dave, SPIA (Signaling Pathway Impact Analysis) is for the analysis of signaling pathways. The ones you tried are metabolic (usually KEGG IDs for metabolic pathways look like 00***). You can use other general gene set enrichment methods that do not use pathway topology information but can be appli ...
written 6.0 years ago by Tarca, Adi570
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Answer: A: SPIA error - Error in density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not
... Hi Ilario, The error: " density.default(pfstmp, bw = sd(pfstmp)/4) : \'bw\' is not positive." occurs when a pathway gets only few DE genes (e.g. 1 or 2) and the pathway in question has only few connections so that the resulting standard deviation of the empirical perturbation accumulations (sd(pfs ...
written 6.0 years ago by Tarca, Adi570
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Negative parameter error when using goseq
... Dear Matthew, I am getting the following error when using goseq. Any idea what may cause it? Thanks, Adi > pwf=nullp(genes,bias.data=cntbias) > gocats=as.list(org.Hs.egGO2ALLEGS) > GOr=goseq(pwf,gene2cat=gocats) Using manually entered categories. Calculating the p-values... Error in dWNCHy ...
go goseq written 6.8 years ago by Tarca, Adi570 • updated 6.8 years ago by Nadia Davidson300

Latest awards to Tarca, Adi

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Making data visible in packages (no visible binding for global variable ...)
Scholar 3.9 years ago, created an answer that has been accepted. For A: SPIA::spia function output
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: SPIA::spia function output

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