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Data uploads

Data upload form

To access the data upload form, click on My Gemma –> Load Data.

Input file formats: profiling data

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 single microarray).

Quick tips to avoid common file format problems

  • Your upload can be compressed. We suggest this as a way to speed up uploads. GZIP and ZIP compression are understood.
  • 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 or “NA”.
  • 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).
  • The row names must match the probe ids in the platform. If they do not match up, the data will be ignored. Gemma will issue warnings about mismatches between probe names in your data and in the platform.
  • Use sensible names for the samples. Later, if you are editing the experimental design, you will want to re-use those names.
  • In the table below, each row represents the expression measurements for one probe (or ‘probe set’). The columns represent different arrays which were run. The top of your data file might look like this (when nicely formatted).
    gene mutant1 mutant2 mutant3 wildtype1 wildtype2 wildtype3
    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, probably for many more lines)

Supported array designs

A list of supported array designs can be found on the Gemma platforms page.If your array is not on the list, contact us.

Data privacy settings

Be default, the uploaded dataset will belong to you and others will not be able to access it. It is possible to make it public or to share the dataset only with a group of collaborators.