Microarray Datafile Information
Currently the Microarray data is provided in text/tab-delimited format. These files can be read with any texteditor program. The recommended way to look at the data is with a spreadsheet program like MS Excel. (A little hint: changing the file ending to .XLS on a PC associates the file with MS Excel and automatically opens it on doubleclicking the icon).
Each column is identified by a header, the order of columns in the file can vary. The following table describes the different column headers and the related data. It is followed by an example dataset.
| HEADER | data |
| EXP | Name of the experiment based on the array id. |
| NAME | Name of the gene or sample that is at a given position. |
| TYPE | Indicates whether an element is a control or cDNA. |
| ACC | The GenBank accession number for an EST generated from the printed cDNA clone (This is the most stable handle for retrieving up to date information about this cDNA clone) |
| CLUS | The UniGene cluster assignment of the EST. This information is not stable and should be disregarded (see above) |
| CH1I | The average total signal for each spot for Cy3 |
| CH1B | The local background calculated for each spot for Cy3 |
| CH1D | The difference between the total and background for each element. |
| CH2I | The average total signal for each spot for Cy5. |
| CH2B | The local background calculated for each spot for Cy5 |
| CH2D | The difference between the total and background for each element. |
| CH2IN | The average total signal for each spot for Cy5 normalized so that the average log ratio of all well measured spots is equal to 0. |
| CH2BN | The local background calculated for each spot for Cy5 normalized so that the average log ratio of all well measured spots is equal to 0. |
| CH2DN | The difference between the total and background for each element normalized so that the average log ratio of all well measured spots is equal to 0. |
| RAT1 | CH1D/CH2D |
| RAT2 | CH2D/CH1D |
| RAT1N | CH1D/CH2DN |
| RAT2N | CH2DN/CH1D |
| CRT1 | and CRT2 Unused. |
| CORR | The correlation of the signal at each pixel of a spot in CH1 to CH2. |
| REGR | The ratio estimated by the slope of the line fit to the distribution of pixels in each spot. |
| RFLAG | Unused. |
| PLAT | The plate ID from which a sample was printed. |
| PROW | The plate row from which a sample was printed. |
| PCOL | The plate column from which a sample was printed. |
| FLAG | A user defined field which identifies spots which are visually of low quality. The value 0 is good all other values represent poor quality spots. |
| CLID | The Identification number of the printed cDNA clone. These are mostly IMAGE clones. It is recommended to verify the clone identity by GenBank lookup using the EST accession number (see above). |
| SPOT | The spot number on the array. |
| LEFT | The left coordinate of the spot on the scanned Microarray Image |
| TOP | The top coordinate of the spot. |
| RIGHT | The right coordinate of the spot. |
| BOT | The bottom coordinate of the spot. |