How do I assess the quality control of Clariom_S_Human CEL files? Preferably using R.

Does the oligo::rma normalization consider the positive and negative controls along with the ERCCs? Can I assume after RMA the normalized arrays are valid? Does the RMA function inform if there is a problem?

After annotation according to the Clariom_S_Human: (“all.eset <- annotateEset(normData, annotation(normData))”) I get the following object:

> ExpressionSet (storageMode: lockedEnvironment) assayData: 27189
> features, 25 samples    element names: exprs  protocolData   rowNames:
> G200 1a G200 2a ... U87 UOV 2 (25 total)   varLabels: exprs dates  
> varMetadata: labelDescription channel phenoData   rowNames: G200 1a
> G200 2a ... U87 UOV 2 (25 total)   varLabels: index   varMetadata:
> labelDescription channel featureData   featureNames: 23064070 23064071
> ... TSUnmapped00000823.hg.1 (27189 total)   fvarLabels: PROBEID ID
> SYMBOL GENENAME   fvarMetadata: labelDescription experimentData: use
> 'experimentData(object)' Annotation: pd.clariom.s.human

There are different featureData that have various names. These is a list of examples from each of these types:

23064070, AFFX-BioB-3_at, ERCCmix1step1, HTA2-neg-47419077_st, HTA2-pos-2824546_st,  TC0100007254.hg.1, TSUnmapped00000823.hg.1

Which of these probes are relevant for differential expression analysis? And which ones can I remove? Only the TC0100007254.hg.1, TSUnmapped00000823.hg.1? How do I need to treat the other probes?

Thank you very much in advance, Kerem