Input file formats: expression or similar data

The “raw” gene expression (or similar) profile data can optionally be loaded into the software for visualization and/or analysis. The correlation-based analysis requires the profile data, while for other analyses it is not needed. Of course ErmineJ doesn’t know what the data you provide means, it can be any matrix of numbers that you want to visualize or analyze.

The data file is a simple tab-delimited text file, with each row representing the dependent variable measurements (e.g., expression levels or ratios) for one set of observations. Each column represents an observation or sample (e.g., a microarray).

Quick tips to avoid common file format problems:

• The input files are tab delimited. Comma or space-delimited files will not work. Exporting files as text from Excel is a good way to produce appropriate files.
• Missing values are ok, but they should be indicated by blanks, not by “NA” or other non-numerical characters. In Excel, they just look like blank cells.
• 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).
• 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 ridiculously detailed instructions.
• All columns and rows must have something written in them, including the “upper left corner”.
• 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.