File Format: CLF (NON-OFFICIAL-RELEASE)

DRAFT

The CLF (cel layout file) maps probe IDs to a particular location in the CEL file. The CLF file is based on version 2 of the TSV file format.

The CLF file is based on version 1 of the TSV file format .

Specs & Features

Deterministic IDs

In many cases, probe IDs are simply enumerated starting with a fixed number by walking through the CEL file in a column or row major order. When this is the case, hints may be provided in the headers which allow the location to be computed from the probe_id. This saves the work of reading the file. When sequential is specified along with col_major order, the the following determines probe IDs:

probe_id = y*cols + x + sequential

And for row_major:

probe_id = x*rows + y + sequential

Parsing and Writing

The official C++ parser used by affy can be found in APT under sdk/file/TsvFile/ClfFile.h. When possible, parsing and writing of CLF files should be done using this code.

Notes

ChipLayout used by APT (in sdk/chipstream) will currently only accept CLF files for which:

In fact all the coordinates are done as row_major and the library files with col_major in the header are due to a bug. Please use row_major going forward.

Example 1

#%chip_type=HuEx-1_0-st-v2
#%chip_type=HuEx-1_0-st-v1
#%chip_type=HuEx-1_0-st-ta1
#%lib_set_name=HuEx-1_0-st
#%lib_set_version=r2
#%create_date=Tue Sep 19 15:18:05 PDT 2006
#%guid=0000008635-1158704285-0732263232-1857033251-0689718480
#%clf_format_version=1.0
#%rows=2560
#%cols=2560
#%sequential=1
#%order=col_major
#%header0=probe_id x y
1 0 0
2 1 0
3 2 0
4 3 0
5 4 0
6 5 0
7 6 0
...

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