(a) What is the difference between spotted and oligonucleotide microarrays?
(b) What is a probe? How are probes for microarrays designed?
(c) What is a probeset? What is probeset summarization and why do we need it?
(d) If a gene is shown to be induced four-fold in a microarray experiment, what would be the log2-transformed expression ratio?
a) In Spotted microarrays, the probes are synthesized prior to deposition on the array surface and are then "spotted" onto glass while in oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames.
b) A probe is a single-stranded sequence of DNA or RNA used to search for its complementary sequence in a sample genome. The probe is placed into contact with the sample under conditions that allow the probe sequence to hybridize with its complementary sequence.
c) A probeset is the set of probes relating to a gene while a probeset summarization is a program for doing background subtraction, normalization and summarizing probe sets from Affymetrix expression microarrays.
d) The log2-transformed expression ratio would be 0.25.