In the SNP copy number analysis, check “Options/Chromosome/User paired normal as reference” to use the signal of the paired normal to obtain the raw copy numbers of tumor samples, as opposed to using the average signal of all normal samples. The normal samples still use their average to get raw copy numbers.

We often observe batch effect in copy number analysis. For example, Arupa Ganguly observed "some arrays hybridized on a different date have a higher copy number for the normal tissue as well as the tumor tissues". If a tumor and its paired normal are in the same batch, we can put them in the standardize group and check “Options/Chromosome/use paired normal as reference”. In this case the normal samples still use their average to get raw copy numbers (may not be good due to batch effect), but tumor samples are adjusted for both batch and individual effect by its paired normal sample.

[Older method] If normal and tumor samples are not paired or they are not in the same batch, but each batch has its own normal samples, it’s best to analyze samples from the same batch together (an "array list file" contains sample of the same batch). After obtaining raw copy numbers, use “Chromosome/Export SNP data” to export raw copy numbers, and finally column-wise combine such raw copy number file of multiple batches and format it as “External data file” and analyze the combined file in a different dChip session (use “Get external data” to read this file).

[V7/22/07+] In copy number analysis, samples of different batches or experiment conditions can use their own normal reference samples. Specify a "RefBatch" column in sample information file with the same value for samples in the same batch or condition. "Ploidy(numeric)" and trimming will work within each "RefBatch". (Discussion)