Update Archives
From ArrayWiki
UPDATE - March 24, 2008 - The ArrayWiki paper will be published in an upcoming issue of BMC Bioinformatics.
UPDATE - September 17, 2007 - We have finally updated our import process and have validated all of the BioPNG encoding schemes. Some experiments now offer a link to reconstruct clean Affymetrix v3 CEL files from our BioPNG-based database. Our next goal will be to upload each of the ~10 Gold-level experiments from GEO (containing raw scanner output DAT files). We will also be creating an extension that will compare clean vs. original gene expression and also PLIER vs. GCRMA calculations. Finally, you may be wondering how to create experiments with BioPNG data. Right now, we recommend that you first create an experiment page (clone an existing page and change ALL information/links), upload your CEL/DAT files in a zip file at caCORRECT and then send an email to biomiblab@bme.gatech.edu providing the file name of the zip that you uploaded and a link to your Wiki page. We will convert all of your data to BioPNG and import the files into the wiki as an on-demand service until we have updated caCORRECT to return BioPNG files as part of the batch process.
UPDATE - August 29, 2007 - Our import progess is proceeding slowly, because we get new ideas for better representations of the data as we go along. We've added the progress meter below and the Data Rank Indicator. We are now automatically extracting scan dates AND timestamps from every Affymetrix sample. We've also added a MetaPage describing BioPNG format.
UPDATE - July 13, 2007 - We currently have 500 experiment descriptions imported from GEO. For an example of the end result of imports for all experiments, please visit Eif3h/WT transcript level or GSE8646. We expect to have over 1000 experiments from GEO in the next week and ~500 experiments from ArrayExpress by the end of July. We expect our quality control process to be running throughout the month of August, updating each page with appropriate quality scores and variance images.
