Analysis of microarray data - VSN International

Opening this menu using Stats |Microarrays | Analyse | One ChannelRegression menu, we would complete thisas to the right to analyse this experimentfor the difference between the control andthe average of the two treatments Line-1and Line-2. The columns from the mainexpression file are entered into theExpression, Slides and Probes fields. Thecolumn FileName is entered into the SlideValidation field, and is used to check thatthe regression terms correspond to theorder of the slides in the main expressionspreadsheet. If the labels do not matchbetween the Slides factor and the SlideOrder Validation entries, this will beflagged as an error in the output. If theorder between the labels and the SlideOrder Validation entries do not match,then a warning will be printed in theoutput and the treatment terms used in theRegression Model field will be sorted into the order thatmatches with the Slides factor. The Slide spreadsheet cancontain multiple variates and factors to be used in theRegression model. Here a variate with just two values, 0 forcontrol entries and 1 for the treated slides has been put intothe model field, and fitting this will create an estimate ofthe difference between the control and the average of Line-1 and Line-2. The Options button opens the options dialogshown to the right can be used to separate out or pool thesums of squares of multiple terms in the regression andcontrol what is printed and the model terms fitted.Analysis of Microarray Data in GenStat 37Use the Store button to save the results from the regressionand to display these in a spreadsheet. This dialog is shownon the following page. Clicking the Run button produces the following output in the Output window andthe spreadsheet on the next page.Regression analysisResponse variate:Fitted terms: Constant, StdvTrtSummary of t and F probabilities% probes with probabilities in the ranges:>10% 5 - 10% 1 - 5% 0.1 - 1%