The in-slide, dye swap and pool's replicate correlations were calculated using the duplicate Correlation function of LIMMA [ 71].
The 46-year-old puppetry artist from New York is known for his 1998 production, "Symphonie Fantastique," which consisted of an hour-long performance of feathers, glitter, plastics, vinyl, mirrors, slides, dyes, blacklight, overhead projections, air bubbles, and latex fishing lures.
For each slide and dye combination the 90% value of the negative controls was used as the detection threshold.
The control and test samples (20 μg RNA in each) were labelled with respectively Cy3-dUTP and Cy5-dUTP (Amersham Pharmacia, Little Chalfont, UK) for the first slide and dye assignment was reversed for the second slide.
Loess normalised technical-replicate data (i.e. data for each spot on each slide, including dye swaps) were used to calculate a mean value of M for each amplicon present on the microarray for each biological replicate.
This generated a total of two technical replicate slides (same dye order) and two dye-reversals slides (opposite dye order).
Colleagues in biology have P.C.R. machines to run and microscope slides to dye; political scientists have demographic trends to crunch; psychologists have their rats and mazes.
We used a Newton algorithm after single slide and dye-swap normalization to assess the 6,724 genes expressed by MVECs for differential expression between SSc-MVECs and N-MVECs.
Gene expression changes in the tammar mammary gland during the reproductive cycle were investigated by a large-scale microarray experiment involving 36 comparisons (72 slides including dye swaps, 144 channels in total) [ 69, 102- 104].
For each species we imported log2-transformed data into SAS version 9 and used 'PROC MIXED' to model and remove systematic sources of variation contributed by Cy3 versus Cy5 dyes, slide and hybridization effects, slide × dye interactions and slide × treatment interactions [ 36, 37].
Out of four, two slides were dye-swaps.
