I'm interested in analyzing microarray data from the article http://www.ncbi.nlm.nih.gov/pubmed/26052715 deposited at GEO here:
even though the data was recently deposited, they were generated from "Glue Grant" Affymetrix chips described in the article http://www.ncbi.nlm.nih.gov/pubmed/21317363
as part of that article, they put available a number of files to facilitate processing of these kind of data here:
and I thought I could build the corresponding pd.* package but unfortunately the *.probeset.csv file that goes on the 'probeFile' slot of the 'AffyGenePDInfoPkgSeed' object is missing and have not been able to find it after googling.
during my googling I found the following BioC post:
that briefly mentions these "Glue Grant" arrays as predecessors of the commercial HTA-2.0 Affymetrix arrays. so i thought i could try to process them using the available pd.hta.2.0 package. however, the CEL files have as chip name 'hGlue_3_0_v1'. This is the header of one of them:
library(affyio) read.celfile.header("GSM1707422_6699_51A_hGlue_3_0_v1_.CEL.gz") $cdfName  "hGlue_3_0_v1" $`CEL dimensions` Cols Rows 2680 2572
so, i decided to download the source of pd.hta.2.0_*.tar.gz, uncompress it, rename the hta.2.0 bits to hGlue_3_0_v1 and package it again as pd.hGlue_3_0_v1_*.tar.gz and try the oligo pipeline.
so far it seems everything to work, which is nice, but i would like to know if 1. anybody has an idea of possible pitfalls with this approach since in principle they are different chips; and 2. if anybody knows where could i access the *.probeset.csv file that goes into the 'probeFile' slot of the 'AffyGenePDInfoPkgSeed' object for these Glue Grant chips, so that i could build the corresponding pd.* package without worrying whether the pd.hta-2.0_*.tar.gz package is the right solution.
thanks!! and happy x-mas everyone!