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I have investigated some of the links to known microarray databases, such as arrayTrack, omnibus (NCBI), TCGA. I find that when trying to get microarray images I either get an exotic file format (such as .sdf or .cel) or text base information. Does anybody know of publicly available microarray images (preferable with metadata too) in .svg, .png, .jpg or another well known image file format?

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  • $\begingroup$ Welcome to Biology.SE I am not quite what exactly you want to be displayed on those images. If you just type microarray on GoogleImages, you'll get many pictures of these dots of colours on a black background. Is it what you're looking for? $\endgroup$ – Remi.b Aug 7 '15 at 20:20
  • $\begingroup$ yes, it is. But I would like them to be available through a database system so I may get a lot of them with description of which genes are on the array. $\endgroup$ – hotGopher Aug 7 '15 at 20:30
  • $\begingroup$ Oh ok. That makes sense. I would tend to guess that researchers rarely upload the pictures directly (as it is a very costly way of storing data) but only the results in a .txt (or other) file (I have never worked with this kind of data). Out of curiosity, why do you want a lot of those pictures? $\endgroup$ – Remi.b Aug 7 '15 at 20:49
  • $\begingroup$ I would like to analyse them on a GPU as I think they are the perfect for data based parallelism. $\endgroup$ – hotGopher Aug 7 '15 at 21:20
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Microarray images (at least for Illumina arrays) will come in .tiff format and are huge compared to the summarized formats (.sdf/.cel). Most places will not archive the raw images (so you won't find them online) and even when you run the microarray, you will often times need to make a special request to output raw images. iirc .jpg images are useless due to compression artifacts.

You can use the proper bioconductor libraries to extract data from the 'exotic' file formats. There are many bioconductor workshops archived online that will go through the steps of microarray analysis.

http://www.bioconductor.org/packages/release/bioc/html/affy.html

http://www.bioconductor.org/packages/release/bioc/html/beadarray.html

http://master.bioconductor.org/help/course-materials/2007/BioC2007/labs/oligo/BioC2007-oligo.pdf

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  • $\begingroup$ sad that its not possible to get raw pictures .. $\endgroup$ – hotGopher Aug 7 '15 at 21:21
  • $\begingroup$ @hotGopher You might to directly contact the authors but that's a pain and it takes time. $\endgroup$ – Remi.b Aug 7 '15 at 23:01

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