User: Saurin D. Jani

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Posts by Saurin D. Jani

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Genes and their associated GO terms and pathways
... Hi Daren, If you have differentially expressed (DE) genes and you know which array type (e.g., hgu133a or any Affy/Agilent expression arrays) you are using...try using GeneMesh. GeneMesh is web-based microarray analysis software at Computational Biology Resource Center (CBRC) of Medical Universi ...
written 9.0 years ago by Saurin D. Jani360
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GeneMesh: Microarray data to Cardiovascular System, Genetic Processes, Immune System Diseases and more...
... Hi BioC, At Proteogenomics Facilty of Medical University of South Carolina, we developed GeneMesh. GeneMesh is a web-based program that uses a database of genes associated with MeSH terms to help investigators mine DNA microarray data to find associations between genes and major MeSH hiearchical d ...
microarray written 9.0 years ago by Saurin D. Jani360
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Answer: A: How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
... Hi there, thanks, Sean and Matin....now it works fantastic....!! Saurin |------------------------------------------------ | Saurin D. Jani | Bioinformatician | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29425 | | Emai ...
written 9.2 years ago by Saurin D. Jani360
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How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
... Dear BioC, Here is my R script code which is running on server in background. ################################## chiptype <- annotation(affy_batch_object); if(chiptype == "hu6800") { library(hu6800cdf); library(hu6800probe); library(hu6800); library(humanCHRLOC); library(humanLLMappings); envG ...
affy written 9.2 years ago by Saurin D. Jani360 • updated 9.2 years ago by Sean Davis21k
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Answer: A: KEGG2heatmap genesymbols as row names?
... About Pathway to HEATMAP # Variable explanation: # esetSub2 = expression matirx # chiptype = annotation found from GeneChip, here 'hgu95a' # envPath2Probes = Environment # envGeneNames <- hgu95aGENENAME; # envPath2Probes <- hgu95aPATH2PROBE; # Generate Pathway Heatmap All_DE_Pathway &l ...
written 9.4 years ago by Saurin D. Jani360
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Answer: A: microarray dataset
... Quoting Weiwei Shi : > Dear Listers: > > I am looking for some microarray dataset publically availabe for research > and can anyone here suggest some resource like that? You can take a look of this: MUSC DNA Microarray Database: http://proteogenomics.musc.edu/ma/musc_madb.php?page=home ...
written 11.3 years ago by Saurin D. Jani360
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yeast2cdf qc.affy(unnormalised, ) I'm Sorry Error: - help,
... Dear BioC, I have downloded and installed BioC 1.7 version of yeast2, yeast2cdf, yeast2probe. When I do QCReport(affybatch)...it gives me error: Computing expression calls... ............done. scaling to a TGT of 100 ... Scale factor for: DS1 0.0423884692508222 Scale factor for: DS2 0.04996660903 ...
yeast2 cdf written 11.7 years ago by Saurin D. Jani360
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Comment: C: searchable archives
... Dear BioC, Searchable Archives helped me in troubleshooting and understading many problems of BioC packages. This service is amazing for open source and open development software project. I like to think this service as "BioC InfoSquare". I have found the searchable archives very helpfull and I wo ...
written 11.7 years ago by Saurin D. Jani360
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Answer: A: p values of significant genes in SAM
... Hi, You can P-values and Q-values as below: sam_p_values <- as.matrix(samoutput at p.value[myDEGenes]); sam_q_values <- as.matrix(samoutput at q.value[myDEGenes]); Replace myDEGenes with character set of All Genes and you can get output of all p-values or q-values of the genes or probeIDs. ...
written 11.7 years ago by Saurin D. Jani360
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annotation hgu133plus2 problem,
... Hi BioC, When I am trying to get annotations of ALL GENEs on my hgu133plus2 GeneChip. Please see below output...here my R script is hanging on computer. I am using Linux 64 bit with 2 GB RAM memory with 45 CEL files. > AnnTable1 <- aafTableAnn(AllGenes,hgu133plus2,AnnCols[2]); Loading requir ...
hgu133plus2 written 11.8 years ago by Saurin D. Jani360 • updated 11.8 years ago by James W. MacDonald45k

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