alastair-droop/checkcel

Rapid validity testing of Affymetrix .CEL files

#checkcel

The checkcel program allows rapid validity testing of Affymetrix .CEL files. The aim of this program is to bulk validate multiple .CEL files from public data.

##Licence

checkcel is released under the GNU General Public License version 3.

##Options & Arguments

checkcel is called as follows:

checkcel [-cfvh] file [...]

• -h: print help
• -v: print version
• -f: filter out invalid .CEL files
• -c: calculate & display intensity statistics

##Output Format

Each output line gives data for a single input file. Output data are tab-delimited. If -f is specified, only valid files are returned, otherwise invalid files are returned with the value unknown. If -c is not specified, the output columns are:

• CEL file name
• file format
• chip ID
• creation algorithm
• row count
• column count
• margin
• outier cell count
• masked cell count

If -c is specified, the following columns are appended to each line:

• minimum intensity value
• maximum intensity value
• unique value count
• invalid value count

##Building checkcel

checkcel should be made by:

cd checkcel
./make