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_endDownload 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_endDownload the sample file here:
http://www.clcbio.com/madata/GEOSampleFileSimpleSequenceTagAndProbe.txt