matrix2png: file format details

This page describes the data file format used by the software. The data file is a tab-delimited text file with one row representing the dependent variable measurements for one set of observations.

Quick tips to avoid common file format problems:

• The input files are tab delimited. Comma or space-delimited files will not work.
• Missing values are okay.
• Notice the 'corner' string in the example below - all columns including the example names have a heading. It does not matter what you put in the corner, but it must not be blank. The parser uses the header to figure out how many features you have, so if you skip the corner string it will appear that you have extra data, resulting in an error message.
• You can only have one column of descriptors, all other data must be your numeric feature data. In other words, don't include extra columns in your file that are not part of the data or the example labels. Extra columns will either result in an error (most likely) or invalid results (if your extra columns look like data).
For microarray analysis, this means that each row represents the expression measurements for one gene. The columns then represent different arrays which were run. It helps in later analysis if the data columns are arranged by condition: for example, put the "wild type" columns all together and the "mutant" columns all together after that. So the top of your data file might look like this (when nicely formatted)

gene	mutant	mutant	mutant	wildtype	wildtype	wildtype
100001_at	-36.3	77.8	64.4	89.4	126.6	86.2
100002_at	1504.2	1512	944.5	1157.9	1652	1358.9
100003_at	845.9	966.5	1057.4	987.4	764.1	878.5
100004_at	2304.4	1991.1	2783.7	1929.8	2236.8	2664.1
100005_at	3826.5	2876.9	4514.1	3187.8	2454.3	3730.6
100006_at	3635	2584.6	3554.9	2810.9	1629	2248.6
100007_at	6328.4	6197.8	7236.4	6224.9	6950	6206.8
100009_r_at	6580.6	8715.9	5280.3	6569.4	8513.4	7236
100010_at	368.2	344.5	-62.4	200	282.7	583.4
100011_at	1949.7	2511.3	1937.8	2684.1	1722.5	2101.3
100012_at	3145.6	2936.7	3358.4	4250.8	2706.4	2776
100013_at	-1098.4	-720.8	-1418.8	-886.9	-764.4	-1247.6
100014_at	1108	1197	985.4	1216.7	1328.1	1161.5
100015_at	6005	1040.6	4434.1	1069.4	864.8	2617.4
100016_at	4485.3	3236.2	4910.2	3474.6	3447.1	3493
100017_at	497.5	399.3	964.2	347.7	524.5	561.3
100018_at	540	1209.7	811.1	1880.8	317.9	587.8
100019_at	-303.5	46.4	0.9	53.4	-252.6	-346.9
100020_at	1606.3	1570.4	1996.6	3319.7	1803.4	1811.7
100021_at	1349.8	1193.5	764.7	331.5	1175	783.9

(etc, possibly for many more lines)

There are a number of things to be careful about in setting up your file

• It must be plain text. In excel, use the "file->save as..." menu selection and then choose "text (tab delimited)" option. Excel will warn you about keeping the file in this format; this is just an annoyance but can be ignored. See "Saving excel files as text" for more detailed instructions.
• All row and column names must not contain spaces. This is because our parsers may get confused by names containing spaces. All columns and rows must have something written in them, including the "upper left corner".
• Missing values are permitted, but each row must have the same number of fields. Files with "ragged" rows are not acceptable. Thus if your data file has missing values at the end of a row, there should be extra tab characters to represent them. One way to fix this is to open the file in a program like Microsoft Excel and resave it as tab-delimited text. Excel adds the extra tab characters.
• The values in the file, other than the row and column labels, must be numbers (no letter or other characters). This means that there can be no other columns of text.