Hi Guido,

It is possible these days to use pdInfoBuilder and oligo for all Affy arrays, even those with only CDFs (see for example the pd.ht.mg.430a package).

Figuring out how to do such things is a non-trivial endeavor however.

> showMethods(makePdInfoPackage)
Function: makePdInfoPackage (package pdInfoBuilder)
object="AffyClariomSPDInfoPkgSeed"
object="AffyExpressionPDInfoPkgSeed"
object="AffyHTAPDInfoPkgSeed"
object="AffyMiRNAPDInfoPkgSeed"
object="AffySNPCNVPDInfoPkgSeed"
object="AffySNPCNVPDInfoPkgSeed2"
object="AffySNPPDInfoPkgSeed"
object="AffySNPPDInfoPkgSeed2"
object="AffySTPDInfoPkgSeed"
object="AffyTilingPDInfoPkgSeed"
object="GenericPDInfoPkgSeed"
object="NgsExpressionPDInfoPkgSeed"
object="NgsTilingPDInfoPkgSeed"

## Uh, let's try 'AffyExpression'

> selectMethod(makePdInfoPackage, "AffyExpressionPDInfoPkgSeed")
Method Definition:

function (object, destDir = ".", batch_size = 10000, quiet = FALSE, 
    unlink = FALSE) 
{
    msgBar()
    cat("Building annotation package for Affymetrix Expression array\n")
    cat("CDF...............: ", basename(object@cdfFile), "\n")
    cat("CEL...............: ", basename(object@celFile), "\n")
    cat("Sequence TAB-Delim: ", basename(object@tabSeqFile), 
        "\n")
    msgBar()
    chip <- chipName(object)

<snip>

## that looks like what we want.

So essentially what one would need is the CDF file, a CEL file, and the tab-delimited sequence file. We can get those using AffyCompatible and GEOquery.

> library(AffyCompatible)
>  rsrc <- NetAffxResource("jmacdon@med.umich.edu", "passwordgoeshere")
> grep("mg-430", names(rsrc), ignore.case = TRUE, value = TRUE)
[1] "HT_MG-430A"   "HT_MG-430B"   "HT_MG-430_PM"
> annos <- rsrc[["HT_MG-430_PM"]]
> sapply(affxAnnotation(annos), force)[c(4,11)]
[[1]]
affxType: CDF 
affxDescription: CDF Library File 
affxFile: AffxFile(1)

[[2]]
affxType: Probe Tabular 
affxDescription: Probe Sequences, tabular format 
affxFile: AffxFile(1)
## this will download the data to a temp dir. Move to your working dir
> readAnnotation(rsrc, annotation = affxAnnotation(annos)[[4]], content = FALSE)
> readAnnotation(rsrc, annotation = affxAnnotation(annos)[[11]], content = FALSE)
## can't be zipped
> unzip("HT_MG-430_PM.probe_tab.zip")
> unzip("/HT_MG-430_PM.cdf.zip")
## get a random CEL file
> getGEOSuppFiles("GSE151727")
## and gunzip one
> gunzip( "GSM4589134_SAMR1_+_Water_1.cel.gz")
## make a seed file
> seed <- new("AffyExpressionPDInfoPkgSeed", cdfFile = "HT_MG-430_PM.cdf", celFile = "GSM4589134_SAMR1_+_Water_1.cel", tabSeqFile = "HT_MG-430_PM.probe_tab")
## and build
> makePdInfoPackage(seed)
================================================================================
Building annotation package for Affymetrix Expression array
CDF...............:  HT_MG-430_PM.cdf 
CEL...............:  GSM4589134_SAMR1_+_Water_1.cel 
Sequence TAB-Delim:  HT_MG-430_PM.probe_tab 
================================================================================
Parsing file: HT_MG-430_PM.cdf... OK
Parsing file: GSM4589134_SAMR1_+_Water_1.cel... OK
Parsing file: HT_MG-430_PM.probe_tab... OK
Getting information for featureSet table... OK
Getting information for pm/mm feature tables... OK
Combining probe information with sequence information... OK
Getting PM probes and sequences... OK
Done parsing.
Creating package in ./pd.ht.mg.430.pm 
Inserting 45141 rows into table featureSet... OK
Inserting 513598 rows into table pmfeature... OK
Inserting 180 rows into table mmfeature... OK
Counting rows in featureSet
Counting rows in mmfeature
Counting rows in pmfeature
Creating index idx_pmfsetid on pmfeature... OK
Creating index idx_pmfid on pmfeature... OK
Creating index idx_fsfsetid on featureSet... OK
Saving DataFrame object for PM.
Saving DataFrame object for MM.
Done.
There were 11 warnings (use warnings() to see them)
## install
>  install.packages("pd.ht.mg.430.pm/", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0'
(as 'lib' is unspecified)
* installing *source* package 'pd.ht.mg.430.pm' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
<snip>

Thank you so much for your answer. I will try to do it as you say!