hi,
It will give you heatmap so, you will see which genes are involved in
those pathways and how their expression intensity look like.
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 <- aafPathway(geneNames(esetSub2), chiptype);
unique(sapply(All_DE_Pathway, length));
pathlist <- do.call("c", All_DE_Pathway);
pathL <- length(pathlist);
pathmatrix <- sapply(pathlist, attributes);
pathnamesX <- unique(t(pathmatrix));
kegg <- as.list(envPath2Probes);
pathRow <- as.numeric(nrow(pathnamesX));
if(pathL >=1)
{
for(i in 1:pathRow)
{
pathID <- pathnamesX[,"id"][i];
pathID <- as.character(unlist(pathID));
pathName <- as.character(unlist(pathnamesX[,"name"][i]));
pathName <- trimWhiteSpace(pathName);
pathName <- sub("/", "_", pathName);
pathName <- sub(" ", "_", pathName);
pathName <- sub(" ", "_", pathName);
pathName <- sub(" ", "_", pathName);
pathName <- sub(" ", "_", pathName);
pathName <- sub("-", "_", pathName);
pathFile <- paste("Pathway",pathName,".jpeg",sep = "_");
pathSub <- paste(pathName,"Legend: Red = High, Blue = Low, White
=
Medium",sep = " ");
pathSub <- paste("Date of Analysis:",date(),pathSub,sep = " ");
Pathway2Heatmap(pathID,pathFile,pathSub); # check out the
function below
}
} # if ends here
#
###########################################################
Pathway2Heatmap <- function(pathway,file,Hsub)
{
kegg <- as.list(envPath2Probes);
pathProbes <- as.matrix(kegg[[pathway]]); # genes extracted from
pathway
esetSub2Genes <- as.matrix(geneNames(esetSub2));
temp <- as.matrix(rbind(unique(esetSub2Genes),unique(pathProbes)));
temp1 <- as.matrix(temp[ as.matrix(duplicated(temp,))]);
exp2 <- esetSub2[temp1];
exp2X <- exprs(exp2);
pathDEGenes <- as.matrix(geneNames(exp2));
pathDEGeneNames <- mget(unique(pathDEGenes),env =
envGeneNames,ifnotfound="No
Annotation For this Probe");
row.names(exp2X) <- pathDEGeneNames;
colnames(exp2X) <- samples;
if (nrow(exp2X) > 1)
{
jpeg(filename= file,width=2000,height=2000);
row.dist <- as.dist(1 - cor(t(exp2X)));
Hsub <- c("Generated by EXAMPLE");
gmpalette <- bluered(64);
heatmap.2(exp2X,col=gmpalette,Colv= FALSE,Rowv =
as.dendrogram(hclust(row.dist,method="centroid")),scale="row",key=TRUE
,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c(
5,85),cexRow=1,cexCol=1,
sub=Hsub,cex.sub=1);
dev.off(which = dev.cur());
print("Pathway Heat map done");
}#if
}#pathway2heatmap
###########################################################
For more info. to run free web based analysis on your data
http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage&
process=Methods_Library_List
Saurin
--- On Tue, 7/29/08, Alberto Goldoni <alberto.goldoni@eurogene.org>
wrote:
From: Alberto Goldoni <alberto.goldoni@eurogene.org>
Subject: [BioC] help for pathways
To: bioconductor-bounces@stat.math.ethz.ch, "Bioconductor"
<bioconductor@stat.math.ethz.ch>
Date: Tuesday, July 29, 2008, 11:08 AM
Hi to everybody,
i have a list of genes and i would like to obtain for all genes
the
pathway in witch it is involved.
there are one script or one package just for it?
--
-----------------------------------------------------
Dr Alberto Goldoni, PhD
Medical Genetics Unit
S. Orsola-Malpighi Hospital
Via Massarenti n.9, Pad 11
40100 Bologna, Italy
Mobile Phone: 338-4145970
Fax: 051-636-4004
alberto.goldoni@eurogene.org
www.eurogene.org
www.lagem.it
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