Substituting Probe ID to Gene Symbols in Pheatmap

Question

[Prateek]

Hello, I have selected top 5 genes using differential analysis from a GSE series and plotted a heatmap using the package pheatmap.

The coding is as follows:

top_genes <- ExcelNew$ID[1:5]

pheatmap(exprs(GEOSeries)[top_genes,],annotation_col = SampleInfo)

The ExcelNew is a data frame which contains 66 probe id in one column mapped with Gene Symbol in different column.

exprs(GEOSeries) contains assay data (expression levels) for each of 36 samples (17AD, 19CTRL) for the GSE series with respect to around 5.5 lakh ID references.

Is it possible to replace these 5 or n number of Probe IDs to Gene Symbols with respect to GENE_SYMBOL in ExcelNew so that instead of Probe IDs on the heatmap, gene symbols are shown.

Thanks

[cpad0112]

join on row.names of exprs(GEOSeries) and ID column of ExcelNew. Remove IDs and make gene symbols as row names. Try exploring labels_row option

[Prateek]

labels_row worked like a charm. Thanks for the reply!