Clusters probes or genes with microarray data (D.B. Baird).
|What to print (
||What to plot (
||Type of clustering to use (
||Distance method to use for hierarchical clustering (
||What type of link to use in hierarchal clustering (
||Criterion to use in forming groups when
||Number of groups to form when
||Grouping threshold for forming groups from the dendrogram; default
||Percentage of the probes/genes to use; default 100|
||Title for the dendrogram|
||Title for the groups plot|
||Whether to use a trellis or single plot (
||Window number for the graphs; default 3|
||Device number on which to plot the graphs|
||What graphics filename template to use to save the graphs; default
||What results to put in spreadsheets (
||Data values (i.e. log-ratios)|
||Identifies the slides|
||Identifies the probes or genes|
||Saves the pair-wise similarities between probes or genes when
||Saves the group membership for each probe|
||Saves the probe or gene amalgamation data when
MAPCLUSTER clusters probes (which may be thought of as representing genes) together on the similarity of their responses over a number of slides or target effects. The
METHOD option specifies whether the clustering is hierarchical, or non-hierarchical using the k-means algorithm. A range of clustering criteria are available for each method (options
CRITERION). The probes are grouped together so that the responses of each group are similar, with the groups as distinct as possible. For the hierarchical clustering, the allocation to groups is specified by using the
GTHRESHOLD option to provide a threshold for the levels of similarity within a group. The dendrogram is then cut at this level, generating an unknown number of groups. For the k-means algorithm, the number of groups must be specified using the
NGROUPS option. The group membership can be saved by the
The log-ratios are supplied by the
DATA parameter. If these are in a single variate, the
SLIDE parameter should supply a factor to index the slides, and the
PROBES parameter should index the probes or genes. Alternatively you can supply a pointer containing a variate for each slide. The slides factor is then not required; if it is given it should just have one entry for each slide in the order of the variates in the pointer. The
PROBES factor is that for a single slide, and all slides must have a common layout.
PLOT option allows you to plot a dendrogram for the hierarchical cluster analyses, but for a large number of probes this is less useful as individual probes cannot be read. The responses of each probe across the targets/slides can also be plotted in a shade plot, but for large numbers of probes this is slow, in which case the mean response for each group can be plotted instead. A spreadsheet containing the grouped data can also be saved using the
With large numbers of probes, the limit of RAM can be quickly reached, so option
PERCENT can be set so that only cluster probes with the largest mean absolute responses are clustered.
By default the plots for the groups are displayed in a trellis arrangement, but you can set option
ARRANGEMENT=single to display them separately, in single plots. The
GTITLE options can supply titles for the dendrogram and groups plot, respectively, and the
WINDOW option specifies the window to use (by default 3). You can use the
DEVICE option to plot to a device other than the screen. The
GRAPHICSFILE option specifies then supplies a template for the file names.
Any restrictions on the
DATA variates are removed.
Commands for: Microarray data.
CAPTION 'MAPCLUSTER example'; STYLE=meta ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH' IF check SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH' " Cluster top 5% Probes from APO Mouse Knock-out Data." MAPCLUSTER [PRINT=summary; PLOT=dendrogram,groups,meangroups;\ METHOD=kmeans; CRITERION=Sums; NGROUPS=16; PERCENT=5;\ ARRANGEMENT=trellis] DATA=cLogRatio; PROBES=NAME; SLIDES=Slide ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF