GEO sample file: using absent/present call and p-value columns for sequence information

The workbench assumes that if there is a third column in the GEO sample file then it contains present/absent calls and that if there is a fourth column then it contains p-values for these calls. This means that the contents of the third column is assumed to be text and that of the fourth column a number. As long as these two basic requirements are met, the sample should be recognized and interpreted correctly.

You can thus use these two columns to carry additional information on your probes. The absent/present column can be used to carry additional information like e.g. sequence tags as shown below:

^SAMPLE = GSM21610
!sample_table_begin
ID_REF      VALUE     ABS_CALL
id1        105.8      AAA
id2        32         AAC
id3        50.4       ATA
id4        57.8       ATT
id5        2914.1     TTA
!sample_table_end
Download the sample file here:
http://www.clcbio.com/madata/GEOSampleFileSimpleSequenceTag.txt

Or, if you have multiple probes per sequence you could use the present/absent column to hold the sequence name and the p-value column to hold the interrogation position of your probes:

^SAMPLE = GSM21610
!sample_table_begin
ID_REF    VALUE    ABS_CALL    DETECTION P-VALUE
probe1    755.07   seq1        1452
probe2    587.88   seq1        497
probe3    716.29   seq1        1447
probe4    1287.18  seq2        1899
!sample_table_end
Download the sample file here:
http://www.clcbio.com/madata/GEOSampleFileSimpleSequenceTagAndProbe.txt