DRAFTThe PS (probeset list file) specifies a list of probeset IDs.
The PS file is based on version 1 of the TSV file format .
Specifications
- Required headers: none
- Optional headers
- chip_type: indicates the chip type (as stored in the CEL file) which the ps file is for. Multiple chip_type headers may be present indicating the ps file can be used with any one of the listed chip types.
- lib_set_name: indicates the name of a collection of related library files for a given chip. For example, the PGF and CLF files intended to be used with this PS file should have the same lib_set_name. Only a single lib_set_name is allowed.
- lib_set_version: indicates the version of a collection of related library files for a given chip. For example, the PGF and CLF files intended to be used with this PS file should have the same lib_set_version. Only a single lib_set_version is allowed.
- create_date: timestamp for when the file was created
- guid: a unique identifier for the fileA
- genome-species: the species represented by this array/list
- genome-version: the version of the genome this list is based on
- genome-version-ucsc: the UCSC genome version
- genome-version-ncbi: the NCBI genome version
- genome-version-date: the approximate date of the genome build
- other headers may be present
- Columns
- per TSV format, order of columns is not guarateed
- per TSV format, additional columns may be present
- probeset_id (required): an integer id >= 0 or charater string of the probeset ID or name.
- other columns may be present
Parsing and Writing
The official C++ parser used by affy can be found in APT under sdk/file/TsvFile/TsvFile.h. When possible, parsing and writing of PS files should be done using this code.
Notes
Nothing at this time.
Example 1 -- Human Exon 1.0 ST Core PS File
#%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
#%genome-species=Homo sapiens
#%genome-version=hg16
#%genome-version-ucsc=hg16
#%genome-version-ncbi=34
#%genome-version-create_date=2003 July
#%guid=0000008635-1158704285-1317760355-0491589515-1257946222
probeset_id
2315252
2315253
2315374
2315375
2315376
2315377
...
Example 2 -- Human Exon 1.0 ST Unmapped Transcripts PS File
Here is another example which includes extra columns of annotation information
#%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=0000008635-1158704285-0806592327-1199287530-0052417134
probeset_id type gi full_accession description
4056516 rescue->FLmRNA->unmapped gi:37181549 gb:AY358219.1 /DEF=Homo sapiens clone DNA188137 RRLF9220 (UNQ9220) mRNA, complete cds. /PROD=RRLF9220
4057777 rescue->FLmRNA->unmapped gi:20530863 gb:AY094596.1 /DEF=Homo sapiens Ras-related protein Rab-7 (RAB7) mRNA, complete cds. /GEN=RAB7 /PROD=Ras-related protein Rab-7
...
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