Use Spot files "HA3.1_clonepos_May04.20060811.txt " & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample and refer to the Sample platform GPL2024 for the clone name
Data processing
Data processing is described in Curtin et al. NEJM, 2005, (353), 2135-3147. Briefly: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system and carried out image and data analysis using UCSF SPOT. The arrays contain 2462 clones printed as triplicate spots. Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. No other computational adjustments were applied to the data. We used the SPROC software to automatically filter the data based on quality criteria, average the log2 ratios of the replicate spots, and assign genome position. Only clones for which two or more spots passed quality criteria and for which the standard deviation of the replicates was less than 0.2 were included in the subsequent analysis. Data were normalized to set the median log2 ratio to zero. We used only clones that were mapped on the genome sequence and which did not detect copy number polymorphisms in normal samples. Data from submission GSE2631 and submission GSE4747 were derived from three different versions of arrays termed HumArray1-3. For compatibility, only data from clones represented on all three versions of the BAC Arrays and that stem from clones that conform to the above criteria are presented in this table.
