aroma-project.org

Q: I work with CEL files from the TCGA project.  I store the data mirroring the TCGA directory structure.  How can work with these CEL files in aroma without having to move or copy them to rawData/?

A: Assume the CEL files are located in:

pathTo/tcgaData/tcga4yeo/tumor/ov/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0/*.CEL

Then, create the link rawData/broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0/GenomeWideSNP_6/ that points to the above TCGA target directory as follows:

target <- "pathTo/tcgaData/tcga4yeo/tumor/ov/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0/";
path <- filePath("rawData", basename(target), "GenomeWideSNP_6");
createLink(path, target=target);

Note that directories rawData/ and rawData/broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0/ will be created automatically, if missing.

Finally, verify that the data set can be located:

cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6");
dataSet <- "broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0";
dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
setFullName(dsR, dataSet);

*The setFullName() command is only need on Windows/if Windows Shortcut links are used.