Author: Baldwin, Don A.; Feldman, Michael; Alwine, James C.; Robertson, Erle S.
Title: Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues Document date: 2014_9_16
ID: xlqdn0c7_32
Snippet: Feature intensities for Cy3 and Cy5 channels were imported into the Partek Genomics Suite (Partek Inc., St. Louis, MO, USA). The average intensity for human intergenic control probes was calculated for cohybridized test and xhh DNA samples, and a scale factor was determined which would make the Cy5 xhh DNA average equal to the Cy3 average. The Cy5 intensities for all PathoChip probes were then multiplied by the scale factor to normalize for diffe.....
Document: Feature intensities for Cy3 and Cy5 channels were imported into the Partek Genomics Suite (Partek Inc., St. Louis, MO, USA). The average intensity for human intergenic control probes was calculated for cohybridized test and xhh DNA samples, and a scale factor was determined which would make the Cy5 xhh DNA average equal to the Cy3 average. The Cy5 intensities for all PathoChip probes were then multiplied by the scale factor to normalize for differences in dye performance. Cy3/Cy5 ratios and Cy3-Cy5 subtractions were calculated for each probe to provide input for dual-channel or single-channel analysis pipelines, respectively. Accession average (AccAvg) was defined as the average Cy3 or Cy5 intensity across all probes for one accession, and accession signal (AccSig) was defined as AccAvg(Cy3) Ϫ AccAvg(Cy5).
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