Does the input file handle replicates?

[jakeyeung]

Hi, I was interested in trying out this clustering package.

Does the input file handle multiple replicates per time points? Or is each column the mean of several replicates at each time point?

Thanks in advance,

Jake

[dadrasarmin]

Hi,

On the help page it addressed this situation as follows:

-i GENE_EXPRESSION_MATRIX [GENE_EXPRESSION_MATRIX ...], --input GENE_EXPRESSION_MATRIX [GENE_EXPRESSION_MATRIX ...]
                        required, e.g. /path/to/gene_expression_matrix.txt
                        or /path/to/gene_expression_matrix.rep1.txt /path/to/gene_expression_matrix.rep2.txt etc.
                        if there are replicates.

                        where the format of the gene_expression_matrix.txt is:

                        gene    1     2    3    ...    time_t
                        gene_1  10    20   5    ...    8
                        gene_2  3     2    50   ...    8
                        gene_3  18    100  10   ...    22
                        ...
                        gene_n  45    22   15   ...    60

                        Note that the first row is a header containing the
                        time points and the first column is an index
                        containing all gene names. Entries are delimited
                        by whitespace (space or tab), and for this reason,
                        do not include spaces in gene names or time point names.