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HenrikBengtsson / aroma.affymetrix

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
https://cran.r-project.org/package=aroma.affymetrix
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question about genome information file #42

Open zhangjsyeah opened 2 years ago

zhangjsyeah commented 2 years ago

hello prof.Bengtsson I write this e-mail want to know that where is the hg18 genome information file about 500K array? I searched dChip data files: [genome information file] at (http://www.hsph.harvard.edu/cli/complab/dchip/snp.htm#genome_info),But didn't exist. I want to know where I can find it? Best wishes Jiashua Zhang

HenrikBengtsson commented 2 years ago

I don't know if the dChip folks still provide them. AFAIK, unless you run dChip like analysis, you won't need them. What is your use case? Do you have an example pipeline that you are trying to follow?

zhangjsyeah commented 2 years ago

Thanks for your reply! The CELL files are used to analyze CNV. (GSM389037.CEL) The CELL files came from Affymetrix 500K array. Now this step (glad <- GladModel (cesNList)) will be run. But appear "Exception: Filed to locate a genome annotation data file for genome"human"" So I didn't how to solve this question? Thanks If you need sample files and a pipeline, I can send you. Thanks again Best wishes JIashuo Zhang

HenrikBengtsson commented 2 years ago

Can you point me a link to the instructions you're following?

zhangjsyeah commented 2 years ago

Thanks for your reply! The pipeline and test sample files (CEL.file) were uploaded here, you can download it. The annotation data included Mapping250K_Nsp_na31_HB20101007.ufl & Mapping250K_sty_na31_HB20101007.ufl, and Mapping250K_Nsp_na31_HB20101007.ugp & Mapping250K_sty_na31_HB20101007.ugp, and Mapping250K_Nsp.cdf & Mapping250K_sty.cdf. These files size so big, cann't be upload. Thanks a lot, best wishes Jiashuo Zhang