Hi,

I am using SCAN.UPC package to get batch effect adjusted intensities for two HGU133Plus2 datasets. However for few probesets I get negative intensity values. I understand that the data is log transformed but is there any way to avoid  that and get the intensities on a linear scale without any negative values?

Also,is it possible to use SCAN.UPC with the Illumina-HT12V4 bead chips?

Thanks.

This should answer your first question: Expression Values for SCAN.UPC?

I'm looking into the possibility of adding support for Illumina and Agilent single-channel arrays, but currently these are not supported. However, you can apply the UPC method to these array types if they have been preprocessed using other methods.

Thanks for the reply.

After the SCAN normalisation I have used the UPC detection method on around 4 different datasets, 3 of which are on affymetrix platform and 1 is on Illumina HT-12 V3 expression beadchip. The distribution of the detection value seems to be on extreme ends that is either 0 or 1 and very few probesets have detection value in the range of 0.1 to 0.9 irrespective of the dataset or the platform used. Can someone help me understand why is this the case? In the UPC paper it is mentioned that anything above 0.5 is considered as detected by the authors, but looking at the graph  0.5 does not look very different then 0.4 or 0.6 cut-off.