Changes between Version 3 and Version 4 of SOPs/integrateExpressionIP


Ignore:
Timestamp:
09/06/17 12:34:32 (7 years ago)
Author:
byuan
Comment:

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  • SOPs/integrateExpressionIP

    v3 v4  
    7575   fisher.test(data)
    7676}}}
     77
    7778'''Method 3'''. Use the GSEA tool from the Broad Institute. Use the raw array data and genes bound as the gene data set to look for enrichment [http://www.broadinstitute.org/gsea/index.jsp GSEA]
     79
     80'''Method 4'''. For visualization, draw a scatterplot on log2 gene expression levels with WT and KO on X and Y axis, highlight the bound genes on top of all genes. This can be achieved with simple R codes. In this example, the two text files each has three columns, with geneID, WT and KO as header. 
     81
     82{{{
     83 control=read.delim("all_genes_exp.txt")
     84 GenesBound = read.delim("GenesBound_exp.txt")
     85 par(pty="s")
     86 plot(log2(control$WT), log2(control$KO))
     87 abline(0,1)
     88 points (log2(GenesBound$WT, log2(GenesBound$KO),  col="red")
     89}}}
     90