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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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Most Affymetrix URLs are broken since now moved to https://www.thermofisher.com/ #29

Open HenrikBengtsson opened 7 years ago

HenrikBengtsson commented 7 years ago

Most Affymetrix URLs are broken since now moved to https://www.thermofisher.com/.

It looks like they're still going to call it Affymetrix Arrays, cf. https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html?icid=fr-affy-main

HenrikBengtsson commented 7 years ago

New locations:

HenrikBengtsson commented 7 years ago

115 URLs that need to be updated:

hb-x1:  ~/repositories/aroma-project.org-website  |develop {2} ?:2 ✗|
→ grep -F "affymetrix.com/" -r content/
content/howtos/createCdfFromBioconductorPlatformDesignInfo/index.md.rsp:ST)](http://www.affymetrix.com/products_services/arrays/specific/hugene_1_0_st.affx#1_6).
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/genomewide_snp5_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/genomewide_snp6_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hugene_1_0_array_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hugene_1_0_array_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hugene_1_0_array_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hugene_1_0_array_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hugene_1_0_array_data.affx>
content/datasets/Affymetrix/index.md.rsp:URL: <https://www.affymetrix.com/analysis/10ksample.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx>
content/datasets/Affymetrix/index.md.rsp:URL: <http://www.affymetrix.com/support/datasets.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx#1_2>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx#1_2>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx>
content/datasets/Affymetrix/index.md.rsp:URL: <http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/copy_number_data.affx>
content/datasets/Affymetrix/index.md.rsp:<http://www.affymetrix.com/support/technical/sample_data/gtc_cytogenetic_data.affx>
content/external/ToolsForAffymetrix/index.md.rsp:<https://www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx>  
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/support/developer/powertools/changelog/>  
content/external/ToolsForAffymetrix/index.md.rsp:URL: <http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=131408>
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/support/developer/tools/devnettools.affx> ("copy
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/products/software/specific/cnat.affx> (Windows
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/products_services/software/specific/genotyping_console_software.affx>
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/support/developer/tools/download_igb.affx>  
content/external/ToolsForAffymetrix/index.md.rsp:Formats](http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/index.html),
content/external/ToolsForAffymetrix/index.md.rsp: URL: <http://www.affymetrix.com/support/developer/fusion/>
content/external/ToolsForAffymetrix/index.md.rsp:URL: <http://www.affymetrix.com/support/developer/tools/devnettools.affx>
content/external/ToolsForAffymetrix/index.md.rsp:<http://www.affymetrix.com/support/developer/tools/devnettools.affx>
content/vignettes/GeneSTArrayAnalysis/index.md.rsp:[www.affymetrix.com](http://www.affymetrix.com/))
content/chipTypes/HT_HG-U133A_and_HT_HG-U133B/index.md.rsp:-   Product page: <http://www.affymetrix.com/support/technical/byproduct.affx?product=ht_hg-u133_set>
content/chipTypes/PrimeView/index.md.rsp:* Product Page: <http://www.affymetrix.com/browse/products.jsp?productId=prod530005>
content/chipTypes/Citrus_SNP/index.md.rsp:Product page: <http://www.affymetrix.com/browse/products.jsp?productId=131428>
content/chipTypes/Axiom_Exome319/index.md.rsp:More at <http://www.axiom.affymetrix.com/>.
content/chipTypes/Axiom_Exome319/index.md.rsp:    <http://www.affymetrix.com/catalog/prod570018/AFFY/Axiom%26%23174%3B+Exome+Genotyping+Arrays#1_1>
content/chipTypes/HG-Focus/index.md.rsp:* Product page: [Human Genome Focus Array](http://www.affymetrix.com/estore/support/technical/byproduct.affx?product=focus)
content/chipTypes/Hs_PromPR_v02/index.md.rsp:-   [Overview](http://www.affymetrix.com/products_services/arrays/specific/human_promoter.affx#1_1)
content/chipTypes/Hs_PromPR_v02/index.md.rsp:    Data](http://www.affymetrix.com/products_services/arrays/specific/human_promoter.affx#1_4)
content/chipTypes/Axiom_MNEc670/index.md.rsp:More at <http://www.axiom.affymetrix.com/>.
content/chipTypes/Axiom_MNEc670/index.md.rsp:    <http://www.affymetrix.com/products_services/arrays/specific/axiom_solution.affx>
content/chipTypes/Cytogenetics_Array/index.md.rsp:* [Product page](http://www.affymetrix.com/products_services/arrays/specific/cytogenetics_solution.affx)
content/chipTypes/Mapping10K_Xba131/index.md.rsp:    materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=10k) (SNP
content/chipTypes/MoEx-1_0-st-v1/index.md.rsp:2006](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle_Print&ID=845557).
content/chipTypes/MoEx-1_0-st-v1/index.md.rsp:file (see [http://www.affymetrix.com/analysis/downloads/current_exon/)](http://www.affymetrix.com/analysis/downloads/current_exon/).
content/chipTypes/MoEx-1_0-st-v1/index.md.rsp:* [Technical Support Documentation](http://www.affymetrix.com/support/technical/byproduct.affx?product=moexon-st)
content/chipTypes/MoEx-1_0-st-v1/index.md.rsp:* [Datasheet](http://www.affymetrix.com/support/technical/datasheets/exon_arraydesign_datasheet.pdf "http://www.affymetrix.com/support/technical/datasheets/500k datasheet.pdf")
content/chipTypes/MoEx-1_0-st-v1/index.md.rsp:* Public data sets: [Tissue / Mixture / Colon Cancer datasets](http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx)
content/chipTypes/Mapping250K_Nsp-and-Mapping250K_Sty/index.md.rsp:-   [Datasheet](http://www.affymetrix.com/support/technical/datasheets/500k_datasheet.pdf)
content/chipTypes/Mapping250K_Nsp-and-Mapping250K_Sty/index.md.rsp:-   [Support Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) (SNP annotation files with SNP positions, dbSNP ID, fragment lengths etc. Probe sequences.)
content/chipTypes/Dm_tiling2_MR_v01/index.md.rsp:    page: <http://www.affymetrix.com/support/technical/byproduct.affx?product=dm_tiling2_mr>
content/chipTypes/HuEx-1_0-st-v2/index.md.rsp:2005](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle&ID=763269).
content/chipTypes/HuEx-1_0-st-v2/index.md.rsp:unsupported [CDF](http://www.affymetrix.com/Auth/support/downloads/library_files/HuEx-1_0-st-v2.cdf.zip)
content/chipTypes/HuEx-1_0-st-v2/index.md.rsp:    Materials](http://www.affymetrix.com/browse/products.jsp?productId=131452&navMode=34000&navAction=jump&aId=productsNav#1_1 "http://www.affymetrix.com/support/technical/byproduct.affx?product=500k") (Library
content/chipTypes/HG_U95ABCDE/index.md.rsp:* [Product page](http://www.affymetrix.com/estore/browse/products.jsp;jsessionid=2292CB3507B7386C16260BF68DF05199?navMode=34000&productId=131538&navAction=jump&aId=productsNav#1_1)
content/chipTypes/MoGene-1_0-st-v1/index.md.rsp:    Array](http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=131476&navAction=jump&aId=productsNav#1_1)
content/chipTypes/MoGene-1_0-st-v1/index.md.rsp:    Set](http://www.affymetrix.com/support/technical/sample_data/gene_1_0_array_data.affx "http://www.affymetrix.com/support/technical/sample data/500k data.affx"),
content/chipTypes/HG-U133A_and_HG-U133B/index.md.rsp:Affymetrix' press release: *Affymetrix Launches First Commercial Human DNA Array to Use Draft Of Human Genome*, [Jan 21, 2001](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle_Print&ID=248283).
content/chipTypes/HG-U133A_and_HG-U133B/index.md.rsp:-   Product page/Support Materials (e.g. CDF): [Human Genome U133 Set](http://www.affymetrix.com/catalog/131536/AFFY/Human-Genome-U133-Set#1_3)
content/chipTypes/miRNA-2_0/index.md.rsp:* Product page: <http://www.affymetrix.com/products_services/arrays/specific/mi_rna.affx>
content/chipTypes/Axiom_GW_Hu_SNP/index.md.rsp:<http://www.axiom.affymetrix.com/>.
content/chipTypes/Axiom_GW_Hu_SNP/index.md.rsp:    <http://www.affymetrix.com/products_services/arrays/specific/axiom_solution.affx>
content/chipTypes/MOUSEDIVm520650/index.md.rsp:-   Product page: <http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=prod100002>
content/chipTypes/Mitochip_2/index.md.rsp:2005](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle_print&ID=797697&highlight=).
content/chipTypes/Mitochip_2/index.md.rsp:    2.0](http://www.affymetrix.com/products/arrays/specific/mito_reseq_2.affx)
content/chipTypes/Mitochip_2/index.md.rsp:    Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=humitoreseq)
content/chipTypes/DMET_Plus/index.md.rsp:    Pack](http://www.affymetrix.com/products_services/arrays/specific/dmet.affx#1_4)
content/chipTypes/GenomeWideSNP_5/index.md.rsp:    page](http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_5)
content/chipTypes/GenomeWideSNP_5/index.md.rsp:-   [Datasheet](http://www.affymetrix.com/support/technical/datasheets/genomewide_snp5_datasheet.pdf)
content/chipTypes/GenomeWideSNP_5/index.md.rsp:    Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_5) (SNP
content/chipTypes/Canine_2/index.md.rsp:    <http://www.affymetrix.com/estore/browse/products.jsp?productId=131425>
content/chipTypes/HG-U133A_2/index.md.rsp:* Product page: <http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133-20>
content/chipTypes/ax13339/index.md.rsp:2007(?). URL: <http://www.affymetrix.com/support/technical/whitepapers/agcc_gridding_whitepaper.pdf>
content/chipTypes/HuGene-1_1-st-v1/index.md.rsp:-   Product page: [Human Gene 1.1 ST Array](http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=131554&navAction=jump&aId=productsNav#1_1)
content/chipTypes/RaGene-1_0-st-v1/index.md.rsp:    Array](http://www.affymetrix.com/products/arrays/specific/ratgene_1_st/ratgene_1_st.affx "http://www.affymetrix.com/products/arrays/specific/100k.affx")
content/chipTypes/RaGene-1_0-st-v1/index.md.rsp:    -   [Gene 1.0 ST Array Data Set](http://www.affymetrix.com/support/technical/sample_data/gene_1_0_array_data.affx "http://www.affymetrix.com/support/technical/sample data/500k data.affx"), Tissue/Mixture.
content/chipTypes/CytoScanHD_Array/index.md.rsp:    page](http://www.affymetrix.com/browse/products.jsp?productId=prod520004&categoryId=35907&productName=CytoScan%22-HD-Array-Kit-and-Reagent-Kit-Bundle#1_1)
content/chipTypes/HG_U95Av2/index.md.rsp:* [Product page](http://www.affymetrix.com/estore/browse/products.jsp;jsessionid=2292CB3507B7386C16260BF68DF05199?navMode=34000&productId=131538&navAction=jump&aId=productsNav#1_1)
content/chipTypes/miRNA-1_0/index.md.rsp: /[Affymetrix](http://www.affymetrix.com/browse/products.jsp?productId=131473&categoryId=35574#1_1)
content/chipTypes/miRNA-1_0/index.md.rsp:* Product page: <http://www.affymetrix.com/products_services/arrays/specific/mi_rna.affx>
content/chipTypes/ATH1-121501/index.md.rsp:Description](http://www.affymetrix.com/estore/browse/products.jsp?productId=131416#1_1))
content/chipTypes/ATH1-121501/index.md.rsp:    Array](http://www.affymetrix.com/estore/browse/products.jsp?productId=131416#1_1)
content/chipTypes/GenomeWideSNP_6/index.md.rsp:    page: <http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_6>
content/chipTypes/GenomeWideSNP_6/index.md.rsp:-   [Datasheet](http://www.affymetrix.com/support/technical/datasheets/genomewide_snp5_datasheet.pdf "http://www.affymetrix.com/support/technical/datasheets/500k datasheet.pdf")
content/chipTypes/GenomeWideSNP_6/index.md.rsp:    Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_6) (SNP
content/chipTypes/MoGene-1_1-st-v1/index.md.rsp:-   Product page: <http://www.affymetrix.com/browse/products.jsp?productId=131555>
content/chipTypes/HT_HG-U133_Plus_PM/index.md.rsp:    Array](http://www.affymetrix.com/products_services/arrays/specific/ht_hgu133_pm_ap.affx#1_4)
content/chipTypes/Mapping50K_Hind-and-Xba240/index.md.rsp:-   Product page: [GeneChip Human Mapping 100K Set](http://www.affymetrix.com/estore/browse/products.jsp?productId=131458&categoryId=35906)  
content/chipTypes/Mapping50K_Hind-and-Xba240/index.md.rsp:    Support Materials: <http://www.affymetrix.com/support/technical/byproduct.affx?product=100k>  (SNP annotation files with SNP positions, dbSNP ID etc. Probe sequences.)
content/chipTypes/Mapping10K_Xba142/index.md.rsp:-   Product page: [GeneChip Human Mapping 10K 2.0  Array](http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=131470)
content/chipTypes/Mapping10K_Xba142/index.md.rsp:-   [Support Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=10k-20)
content/chipTypes/Mapping10K_Xba142/index.md.rsp:-   Images: [Coverage](http://www.affymetrix.com/en/images/10k2_enlargement.gif)
content/chipTypes/Rat230_2/index.md.rsp:page](http://www.affymetrix.com/estore/catalog/131492/AFFY/Rat-Genome-230-2.0-Array)
content/chipTypes/Test3/index.md.rsp:    <http://www.affymetrix.com/support/developer/fusion/>
content/chipTypes/DroGene-1_0-st-v1/index.md.rsp:Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=modelorg_1_1_array)
content/chipTypes/Citrus/index.md.rsp:page: <http://www.affymetrix.com/browse/products.jsp?productId=131428>
content/chipTypes/Mm_PromPR_v02/index.md.rsp:-   <http://www.affymetrix.com/estore/browse/products.jsp?productId=131480&categoryId=35749#1_3>
content/chipTypes/HTA-2_0/index.md.rsp:    <http://www.affymetrix.com/estore/browse/products.jsp?productId=prod760002&categoryId=35676&productName=GeneChip%2526%2523174%253B-Human-Transcriptome-Array-2.0#1_1>
content/chipTypes/HuGene-1_0-st-v1/index.md.rsp:    Array](http://www.affymetrix.com/estore/browse/products.jsp?productId=131453)
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:2006](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle_Print&ID=845557).
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:<http://www.affymetrix.com/analysis/downloads/current_exon/>).  Consult
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:    page](http://www.affymetrix.com/products/arrays/specific/rat_exon.affxhttp://www.affymetrix.com/products/arrays/specific/rat_exon.affx)
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:-   [Datasheet](http://www.affymetrix.com/support/technical/datasheets/exon_arraydesign_datasheet.pdf)
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:    Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=moexon-st)
content/chipTypes/RaEx-1_0-st-v1/index.md.rsp:    datasets](http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx)
content/chipTypes/HG-U133_Plus_2/index.md.rsp:[2003-10-02](http://investor.affymetrix.com/phoenix.zhtml?c=116408&p=irol-newsArticle&ID=454699)
content/chipTypes/HG-U133_Plus_2/index.md.rsp:    Array](http://www.affymetrix.com/products/arrays/specific/hgu133plus.affx)
content/chipTypes/HG-U133_Plus_2/index.md.rsp:-   [Datasheet](http://www.affymetrix.com/support/technical/datasheets/human_datasheet.pdf)
content/chipTypes/HG-U133_Plus_2/index.md.rsp:    Materials](http://www.affymetrix.com/support/technical/byproduct.affx?product=hg-u133-plus)
content/chipTypes/CytoScan750K_Array/index.md.rsp:* [Product page](http://www.affymetrix.com/browse/products.jsp?navMode=34000&productId=prod570043)
content/chipTypes/X_laevis_2/index.md.rsp:-   [Product  page](http://www.affymetrix.com/browse/products.jsp?productId=131525&navMode=34000&navAction=jump&aId=productsNav#1_1)
content/chipTypes/HT_MG-430_PM/index.md.rsp:-   Product page: <http://www.affymetrix.com/estore/browse/products.jsp?productId=131444&categoryId=35605>
content/resources/external/index.md.rsp:URL: <https://www.affymetrix.com/community/forums/index.jspa>
content/resources/external/index.md.rsp:- [Affymetrix Data Files](http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/index.html), Affymetrix Developers Network.
content/presentations/index.md.rsp:<http://www.affymetrix.com/corporate/events/low_level_workshop/2007_04_low_level_workshop.affx>