Hi all. I have such a basic question, I apologise. I am starting my first gene expression meta-analysis. I have a set of microarrays of interest from GEO. I am copying the protocol of a paper that says:
"The vast majority of studies were single channel intensity data from Affymetrix microarrays. One study was done using spotted cDNA microarray, but was included since the signal intensity from young and old pairs of species compared in original report were available. Studies in which data was obtained from a set of genes in a highly biased fashion (e.g. custom arrays featuring only genes associated with a given pathway) were excluded."
I want to know whether my studies are also almost single channel intensity data, to make my analysis as comparable as possible to their paper. have the name of each microarray used (e.g. Affymetrix Murine Genome U74B Version 2 Array, Illumina MouseRef-8 v2.0 expression bead chip). In addition, I know how each microarray was generated (e.g. in situ oligonucleotide, oligonucleotide beads, spotted DNA/cDNA, spotted oligonucleotide).
For some of these, I know the microarrays are "GeneChip". I read somewhere that all GeneChips are single channel intensity. Can I ask (1) Are all GeneChips single channel intensity? and (2) for the two examples above, how would I find out if these are single-channel intensity (the description on GEO does not say GeneChip, and I can't find information about single channel on Affymetrix/Illumina website)? Can I tell whether something is single channel based on the method used to generate each microarray (e.g. in situ oligonucleotide, spotted cDNA)?
GeneChip is the trademark for Affymetrix arrays.
You should be able to locate a "platform number" for array datasets that you are interested in. When you search GEO with that platform number you will get detailed information about that array type. Here is one example.
Thank you. Yes I can get to that page as in your example (that's the page that I originally used to pull down the information about the microarray). But I can't find where specifically on that page, or on links from that page, where it describes whether it is single channel or not? I'm wondering if "single channel" could also be described by another phrase that I don't know about?
As I recall (for expression arrays): Affymetrix arrays were single channel/one color. Agilent arrays could be used as single color (only one sample) or two color (with two samples). Illumina arrays were single channel/color. One could always spot ones own arrays (people did that a lot before commercial entities took over). They could be used in one/two color modes.