Clusters microarray slides (D.B. Baird).
|What to print (
||What to plot (
||What distance method to use to form the similarity matrix (
||Percentage of the probes/genes to use to calculate correlations; default 100|
||Title for the dendrogram|
||Title for the minimum spanning tree|
||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
||Data values (i.e. log-ratios)|
||Identifies the slides|
||Identifies the probes or genes|
||Saves the correlation matrix|
||Saves the distance matrix|
MASCLUSTER clusters microarray slides (or targets) together on the similarity of their responses over a number of probes or genes. The slides are grouped together so that the pattern of responses over the probes/genes are similar, with the groups as distinct as possible.
DMETHOD option specifies the distance method to use to form the similarity matrix: either
With large numbers of probes or genes, many may be non-informative, only being subject to random variation. So the
PERCENT option controls the percentage of the probes to use: if
PERCENT is less than the default 100,
MASCLUSTER uses only the top
PERCENT of probes according to their mean absolut response.
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.
MTITLE options can supply titles for the plots of the dendrogram and minimum spanning tree, 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 'MASCLUSTER example'; STYLE=meta ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH' IF check SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutStacked.GSH' " Cluster Slides from APO Mouse Knock-out Data." MASCLUSTER [PRINT=correlations,cluster; PLOT=dendrogram;\ DMETHOD=correlation; PERCENT=10] DATA=cLogRatio;\ SLIDES=Slide; PROBES=NAME ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF