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SOMClust |
| Input | |
| SelTag data | Input file in seltag format |
| Fields select |
List of fields -
List of expression fields (tissues) used to calculate correlation between gene expression profiles,
namely field indices in data format of input file starting from 1 (column numeration is not depend on
the Case Names option).
Examples of input: 1;2;3-7;12; 1-12; Fields list - Filename for fields selection in XML format. This is another way to set the list of fields. |
| Genes for select | Genes for select
- List of genes to calculate correlation, namely gene indices in data set of input file starting from 1
(column numeration is not depend on the Case Names option).
Examples of input: 1;2;3-7;12; 1-12; Gene list - Filename for genes selection in XML format for Gene List. This is another way to set the list of genes. |
| Output | |
| Result | Name of output file |
| options | Number of rows in grid This parameter defines number of rows in the map |
| Number of columns in grid | This parameter defines number of columns in the map |
| Options | |
| Select clustering objects | Select clustering objects: genes or samples |
| Type of distance | Type of distance between expression profiles. Several types of correlations are possible: 1-rij; 1-|rij|; 1+rij; Squared Euclidian distance; Euclidian distance; Manhattan distance; Chebyshev distance. |
| Missing data treatment | Option to treat missing data. Several options are possible: Substitute by means (missing data are substituted by expression means in corresponding field); Case-wise deletion (correlations/distances are calculated by excluding cases that have missing data for any of the selected variables, all correlations are based on the same set of data); Pair-wise deletion (correlations/distances between each pair of profiles are calculated from all fields/samples having valid data for those two profiles). |
| Maximal number of iterations | Maximal number of iterations to perform SOM clustering. |