AB1700 data

Set which column from the raw data file that should be used to calculate the final data matrix, select one of the arrays by clicking on a . Set Channel 1 to Assay_Normalised_Signal

Base Sample

If you want to use a base array as common reference for all your arrays, select which array you want to use at Base Sample.

Quantile Normalise All Arrays

Quantile normalisation (Bolstad et al 2002) makes different arrays comparable by making sure that the distribution of intensities are the same across arrays. The normalisation distribution is chosen by averaging each quantile across chips.

Experiment

Select the preferred values for the combo-boxes at Combine in-array replicates, combine method, and Result Data.

• Combine in-array replicates means that replicates on the same array will be combined in some way, so that they are all represented by just one value. If you choose not to combine them, you will get one row for each replicate in your final data matrix. This means that a gene with two replicates on the same array will appear twice in the final matrix. If the Combine in-array replicates is set to yes, remember to also set which method to used to combine the replicates.
• If you want to use the intensities directly, set Result data to None (you should then log2 transform your data later). If you are using a common reference for your arrays, you should select log ratio for the final matrix.