search

WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
Other
89 stars 53 forks source link

Missing files from affymetrix website #96

Closed e-sollier closed 1 year ago

e-sollier commented 1 year ago

Hello,

I would like to process CEL files from Affymetrix arrays (SNP6.0 and 500k). I tried to follow the tutorial at https://penncnv.openbioinformatics.org/en/latest/user-guide/affy/ but this requires downloading http://www.affymetrix.com/Auth/support/downloads/library_files/genomewidesnp6_libraryfile.zip , which results in an error 404 for me.

Is it possible to download this data from elsewhere, or is there any other solution ?

Thanks in advance for your help.

kaichop commented 1 year ago

The 500K and 6.0 arrays are quite old, so I would guess the URL has changed. I would suggest that you explore the Affymetrix website a bit to see whether there are other places to download library files or even directly email them to find it.

On Wed, Oct 26, 2022 at 9:10 AM Etienne Sollier @.***> wrote:

Hello,

I would like to process CEL files from Affymetrix arrays (SNP6.0 and 500k). I tried to follow the tutorial at https://penncnv.openbioinformatics.org/en/latest/user-guide/affy/ but this requires downloading http://www.affymetrix.com/Auth/support/downloads/library_files/genomewidesnp6_libraryfile.zip , which results in an error 404 for me.

Is it possible to download this data from elsewhere, or is there any other solution ?

Thanks in advance for your help.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/96, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OANEJS4U6LRBW6CK6LWFEUT5ANCNFSM6AAAAAARO7LRAI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

e-sollier commented 1 year ago

Thanks for the suggestion! I indeed managed to find the Affymetrix library files at https://www.thermofisher.com/de/de/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html. For example the 6.0 data can be downloaded from https://sec-assets.thermofisher.com/TFS-Assets/LSG/Support-Files/genomewidesnp6_libraryfile.zip. Perhaps the link in https://penncnv.openbioinformatics.org/en/latest/user-guide/affy/ could be updated, so that other users do not face the same issue.

kaichop commented 1 year ago

Thank you. The links are updated.

On Wed, Oct 26, 2022 at 11:37 AM Etienne Sollier @.***> wrote:

Closed #96 https://github.com/WGLab/PennCNV/issues/96 as completed.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/96#event-7674083761, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGFS7TV7C3V5HCGHV3WFFF2HANCNFSM6AAAAAARO7LRAI . You are receiving this because you commented.Message ID: @.***>

suyanxun commented 1 year ago

Thanks for the suggestion! I indeed managed to find the Affymetrix library files at https://www.thermofisher.com/de/de/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html. For example the 6.0 data can be downloaded from https://sec-assets.thermofisher.com/TFS-Assets/LSG/Support-Files/genomewidesnp6_libraryfile.zip. Perhaps the link in https://penncnv.openbioinformatics.org/en/latest/user-guide/affy/ could be updated, so that other users do not face the same issue.

I can not get the file from https://sec-assets.thermofisher.com/TFS-Assets/LSG/Support-Files/genomewidesnp6_libraryfile.zip, could you share it? thanks