Due to the shifting of objects over the clusters for the different
methods, it is possible that the same gene is found significant for a
different cluster in another method. These can be tracked with the
FindGenes function. Per method and per cluster, it will take note of
the genes found significant and investigate if these were also find for
another cluster in another method.
Preferably an output of the
Optional. Names of the methods. Default is NULL.
The returned value is a list with an element per cluster and per cluster one for every gene. Per gene, a vector is given which contain the methods for which the gene was found. If the cluster is changed compared to the reference method of DataLimma, this is indicated with an underscore.
Marijke Van Moerbeke
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data(fingerprintMat) data(targetMat) data(geneMat) MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE, method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE) MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE, method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE) MCF7_DiffGenes_FandT10=DiffGenes(list(MCF7_F,MCF7_T),Selection=NULL,geneExpr=geneMat, nrclusters=7,method="limma",sign=0.05,top=10,fusionsLog = TRUE, weightclust = TRUE, names = NULL) MCF7_SharedGenes=FindGenes(dataLimma=MCF7_DiffGenes_FandT10,names=c("FP","TP"))
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