Currently the data import allows the header in the expression_table.txt to hold information about the biological condition a replicate (a column) belongs to, e.g. the following column name
Wildtype-Leaf_1*MinutesAfterHeatshock_1*1
specifies that the expression values in this column were assessed for a RNA sample obtained from a
- wildtype plant and leaf 1 (group),
- sampling RNA one minute after exposing the plant to heat shock (sample),
- and that this column is the biological replicate
1 of these two group and sample conditions.
In fact, we have two groups (experimental or biological factors) here:
The genotype (wildtype, knockout XYZ) and the tissue sampled (leaf 1, leaf 3, ...).
Ideally we can distinguish any number of groups by applying the * separator as often as required to retain n groups-levels and just a single level of samples and a single level of replicates. Note that these levels refer to the tree structure implied.
Be careful when implementing this, because this effects many other functions; among them the principal component analysis.
Currently the data import allows the header in the
expression_table.txtto hold information about the biological condition a replicate (a column) belongs to, e.g. the following column nameWildtype-Leaf_1*MinutesAfterHeatshock_1*1specifies that the expression values in this column were assessed for a RNA sample obtained from a
1of these two group and sample conditions.In fact, we have two groups (experimental or biological factors) here:
The genotype (wildtype, knockout XYZ) and the tissue sampled (leaf 1, leaf 3, ...).
Ideally we can distinguish any number of groups by applying the
*separator as often as required to retainngroups-levels and just a single level of samples and a single level of replicates. Note that these levels refer to the tree structure implied.Be careful when implementing this, because this effects many other functions; among them the principal component analysis.