Uploading your own data: In order to use
ArrayMining.net with your own data there are two possibilities:
Option 1: You can
upload a tab- or
space-delimited text-file containing pre-normalized Microarray
data in the following simple matrix-format (see Fig. 1):
gene expression matrix
You can download an example data file here (use right-click and "Save as"). The
columns must correspond to the samples and the rows to the genes.
The first column contains the gene identifiers (a unique label
per gene) and the last row the class information for the samples
(multiple samples can have the same class label). The rest of the
matrix should contain normalized expression values obtained using
any of the common Microarray normalization methods (e.g. VSN,
RMA, GCRMA, MAS, dChip, etc.). The gene identifiers can be
any one of the following: Affymetrix ID, ENTREZ ID, GENBANK ID.
You can also use your own identifiers; however, in this case you
won't obtain any links to functional annotation data bases. The
class labels can be any alphanumeric strings or symbols
(e.g. "tumour" and "healthy", or "1","2", "3", or "leukemia1",
"leukemia2", "leukemia3", etc.). Samples belonging to the same
class need to have exactly the same class label. The last row
containing the class labels has to begin with a user-defined
"sample type"-label, e.g. "phenotypes", "tumours" or just
"labels". Optionally, unique IDs per sample can be specified
in the first row (if this line is missing, the samples
will be numbered consecutively).
Option 2: You can upload
a compressed ZIP-archive containing Affymetrix CEL-files
and a txt-file containing tab-delimited numerical sample labels (specifying
replicates by the same number, i.e. "1 1 1 2 2 2" for an experiment
with 6 samples, two classes and three samples for both class 1 and class 2)
Please contact us, should you experience any kind of problems when uploading or analyzing your data.