Hi everyone,

I'd very much appreciate any help/advice you can offer. I am trying to analyse publically available 3' microarray data - available here https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6969/?array=A-MTAB-599

• I have an array annotation txt file but no cdf file. When I run this code:

**library(affy)
library(limma)
library(Biobase)
celpath = "C:/Users/hp/Documents/Research/DDIR/raw data/DDIR CEL"
data = ReadAffy(celfile.path=celpath)
data**

• I get:

>AffyBatch object
>size of arrays=1164x1164 features (130 kb)
>cdf=ADXECv1a520743 (??? affyids)
>number of samples=273
>Error in getCdfInfo(object) : 
  >Could not obtain CDF environment, problems encountered:
>Specified environment does not contain ADXECv1a520743
>Library - package adxecv1a520743cdf not installed
>Bioconductor - adxecv1a520743cdf not available
>In addition: Warning message:
>missing cdf environment! in show(AffyBatch) 

• I tried to install the package:

**BiocManager::install("adxecv1a520743cdf")**

• But got this error:

>  package ‘adxecv1a520743cdf’ is not available (for R version 3.6.1) 

• I'm at a bit of a loss as to what to try next. Any help would be very much appreciated! Thank you :)

• This is my session info

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] pdInfoBuilder_1.48.0        affxparser_1.56.0           RSQLite_2.1.2              
 [4] oligo_1.48.0                oligoClasses_1.46.0         makecdfenv_1.60.0          
 [7] affyio_1.54.0               genefilter_1.66.0           Biostrings_2.52.0          
[10] XVector_0.24.0              survminer_0.4.6             ggpubr_0.2.3               
[13] magrittr_1.5                survival_2.44-1.1           gridExtra_2.3              
[16] glmnet_2.0-18               foreach_1.4.7               Matrix_1.2-17              
[19] MASS_7.3-51.4               pheatmap_1.0.12             EnhancedVolcano_1.2.0      
[22] ggrepel_0.8.1               DESeq2_1.24.0               SummarizedExperiment_1.14.1
[25] DelayedArray_0.10.0         BiocParallel_1.18.1         matrixStats_0.55.0         
[28] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0         reshape_0.8.8              
[31] RColorBrewer_1.1-2          org.Mm.eg.db_3.8.2          AnnotationDbi_1.46.1       
[34] IRanges_2.18.3              S4Vectors_0.22.1            Biobase_2.44.0             
[37] BiocGenerics_0.30.0         gplots_3.0.1.1              Glimma_1.12.0              
[40] edgeR_3.26.8                limma_3.40.6                readxl_1.3.1               
[43] forcats_0.4.0               stringr_1.4.0               dplyr_0.8.3                
[46] purrr_0.3.2                 readr_1.3.1                 tidyr_1.0.0                
[49] tibble_2.1.3                ggplot2_3.2.1               tidyverse_1.2.1            
[52] NormExpression_0.1.0       

loaded via a namespace (and not attached):
 [1] backports_1.1.5        Hmisc_4.2-0            plyr_1.8.4            
 [4] lazyeval_0.2.2         splines_3.6.1          digest_0.6.21         
 [7] htmltools_0.4.0        gdata_2.18.0           checkmate_1.9.4       
[10] memoise_1.1.0          cluster_2.1.0          annotate_1.62.0       
[13] modelr_0.1.5           colorspace_1.4-1       blob_1.2.0            
[16] rvest_0.3.5            haven_2.1.1            xfun_0.11             
[19] crayon_1.3.4           RCurl_1.95-4.12        jsonlite_1.6          
[22] zeallot_0.1.0          zoo_1.8-6              iterators_1.0.12      
[25] glue_1.3.1             gtable_0.3.0           zlibbioc_1.30.0       
[28] scales_1.0.0           DBI_1.0.0              Rcpp_1.0.2            
[31] xtable_1.8-4           htmlTable_1.13.3       foreign_0.8-71        
[34] bit_1.1-14             preprocessCore_1.46.0  km.ci_0.5-2           
[37] Formula_1.2-3          htmlwidgets_1.5.1      httr_1.4.1            
[40] acepack_1.4.1          ff_2.2-14              pkgconfig_2.0.3       
[43] XML_3.98-1.20          nnet_7.3-12            locfit_1.5-9.1        
[46] tidyselect_0.2.5       labeling_0.3           rlang_0.4.0           
[49] munsell_0.5.0          cellranger_1.1.0       tools_3.6.1           
[52] cli_2.0.0              generics_0.0.2         broom_0.5.2           
[55] knitr_1.26             bit64_0.9-7            survMisc_0.5.5        
[58] caTools_1.17.1.2       nlme_3.1-140           xml2_1.2.2            
[61] compiler_3.6.1         rstudioapi_0.10        ggsignif_0.6.0        
[64] geneplotter_1.62.0     stringi_1.4.3          lattice_0.20-38       
[67] KMsurv_0.1-5           vctrs_0.2.0            pillar_1.4.2          
[70] lifecycle_0.1.0        BiocManager_1.30.10    data.table_1.12.4     
[73] bitops_1.0-6           R6_2.4.1               latticeExtra_0.6-28   
[76] affy_1.62.0            KernSmooth_2.23-15     codetools_0.2-16      
[79] gtools_3.8.1           assertthat_0.2.1       withr_2.1.2           
[82] GenomeInfoDbData_1.2.1 hms_0.5.2              rpart_4.1-15          
[85] lubridate_1.7.4        base64enc_0.1-3  

GEO has the cdf:

> library(GEOquery)
> library(makecdfenv)
> download.file("https://www.ncbi.nlm.nih.gov/geo/download/?acc=GPL23985&format=file&file=GPL23985%5FADXECv1a520743%2Ecdf%2Egz", "ADXECv1a520743.cdf.gz")
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GPL23985&format=file&file=GPL23985%5FADXECv1a520743%2Ecdf%2Egz'
Content type 'application/octet-stream' length 21705104 bytes (20.7 MB)
downloaded 20.7 MB

> gunzip("ADXECv1a520743.cdf.gz")

> make.cdf.package("ADXECv1a520743.cdf", species = "Homo sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 1110 dots..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Creating package in C:/Users/jmacdon/Desktop/adxecv1a520743cdf 



README PLEASE:
A source package has now been produced in
C:/Users/jmacdon/Desktop/adxecv1a520743cdf.
Before using this package it must be installed via 'R CMD INSTALL'
at a terminal prompt (or DOS command shell).
If you are using Windows, you will need to get set up to install packages.
See the 'R Installation and Administration' manual, specifically
Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset'
for more information.

Alternatively, you could use make.cdf.env(), which will not require you to install a package.
However, this environment will only persist for the current R session
unless you save() it.

> install.packages("adxecv1a520743cdf/", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.6'
(as 'lib' is unspecified)
* installing *source* package 'adxecv1a520743cdf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'adxecv1a520743cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'adxecv1a520743cdf'
** help
*** installing help indices
  converting help for package 'adxecv1a520743cdf'
    finding HTML links ... done
    adxecv1a520743cdf                       html  
    adxecv1a520743dim                       html  
    geometry                                html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'adxecv1a520743cdf'
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'adxecv1a520743cdf'
*** arch - x64
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'adxecv1a520743cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'adxecv1a520743cdf'
** testing if installed package can be loaded from final location
*** arch - i386
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'adxecv1a520743cdf'
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'adxecv1a520743cdf'
*** arch - x64
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'adxecv1a520743cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'adxecv1a520743cdf'
** testing if installed package keeps a record of temporary installation path
* DONE (adxecv1a520743cdf)

After which you should be good to go.