Analysis of microarray data - VSN International

Analysis of Microarray Data in GenStat 35One channel ANOVAThe One Channel ANOVA menu performs an analysis of variance on all the probes/genes in parallel. Itassumes a single value from each slide, as with Affymetrix chips. The treatment structure across the slidesneeds to be provided in a small spreadsheet that supplements the main spreadsheet. A wide range ofstatistics from the ANOVA can be saved on each gene, and these can be saved in a spreadsheet.Using the expression values from “Hyb-Expressions.gsh”, we need aspreadsheet that gives the treatments on the various slides. This has beenentered into the spreadsheet to the right, which only contains two columns,FileNames – the labels of the slides in the main spreadsheet, and Target –the targets (treatments) applied to the 9 slides. This experiment had threereplicates of three treatments, a standard control line and two experimentallines that were to be compared with the control. This Slide informationspreadsheet has been saved as “HybFiles.gsh”.Opening this menu using Stats | Microarrays | Analyse | One ChannelANOVA menu, we would complete this as to theright to analyse this experiment. The columns fromthe main expression file are entered into theExpression, Slides and Probes fields. The columnFileName is entered into the Slide Validation field,and is used to check that the treatment factorscorrespond to the order of the slides in the mainexpression spreadsheet. If the labels do not matchbetween the Slides factor and the Slide OrderValidation entries, this will be flagged as an error inthe output. If the order between the labels and theSlide Order Validation entries do not match, then awarning will be printed in the output and theTreatment factors used in the Treatment and BlockStructure fields will be sorted into the order that matches with the Slides factor. The Slide spreadsheet cancontain multiple Treatment and Block factors and the same types of treatment structures can be entered inthe Treatment and Block Structure fields as in the standard ANOVA menu. For example, if the slides hadbeen grouped into three replicates, we could have a factor Rep in the Block Structure field to removebetween replicate differences. As this trial is being treated as a completely randomized experiment, theBlock Structure field is left blank. If we had a factorial arrangements of two treatments (A and B) wecould enter A*B as the Treatment Structure, and if we had 4 separate cell lines, two treated with onechemical, and two with another, we could use the nested structure Chemical/CellLine. See the Stats |Analysis of Variance | General menu for more details on treatment and block structures.Contrasts been the treatment levels can also be defined using theContrasts button. These are added to the Treatment Structure fieldas COMP, REG, or POL functions. The COMP and REG functionsrequire contrast matrices that are produced when the OK button ispressed on the dialog opposite.