I have come across the dataset GSE15852 which is an expression dataset from human breast tumors and their paired normal tissues.
The microarray study was done on platform GPL96 [HG-U133A]. I want to know where can I get more detailed documentation about GPL96 and which are the gene probes (out of 22283 probes, 14500 are gene probes according to this document http://www.carrerasresearch.org/es/genechip-human-genome-u133-arrays_38699.pdf )?
What role does the control probes AFFX-r2-Bs-lys-3_at , AFFX-r2-Hs18SrRNA-3_s_at etc play ?
Can anyone please point out to a more explanatory tutorial for microarray data platforms?
Thanks in advance.
Probes are the complementary sequence for the gene, which on hybridization bind to complementary regions of the gene and the intensity is captured by the scanner.
yes probes are that. but are all the probes in an affymetrix microarray target genes? or are there other probes also? I need the gene expression data columns only.
some probes may not have annotation, check the GPL96 for complete probe details.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL96
download full table from above link, it has all the probe details.
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