hi, I'm new to microarrays data analysis. I was just given one txt.file and was told to do an analysis with "beadarray". Unfortunately nobody around is familiar with any of this.
this file at hand (200669330043_all.raw.txt) has all 12 sections of the array included. the following columns plus mean sd etc of the other sections (B-L) are registered.
ProbeID, 200669330043A.mean, 200669330043A.sd ,200669330043A.nbeads, 200669330043A.nouts 200669330043A.nbad 200669330043A.pvalue TargetID QC Species Source SearchKey Transcript ILMNGene SourceReferenceID RefSeqID UnigeneID EntrezGeneID GI Accession Symbol ProteinProduct ProbeId ArrayAddressId ProbeType ProbeStart ProbeSequence Chromosome ProbeChrOrientation ProbeCoordinates Cytoband Definition OntologyComponent OntologyProcess OntologyFunction Synonyms ObsoleteProbe_Id Factor nuID
the dim when read in by simply read.csv is dim(data) [1] 48107 105
I tried to reproduce pretty much anything from "BeadArrayUseCases" but failed even to read in the data. I thought this to be already some kind of summary and therefore tried to read it by read.ilmn of the limma package. there is no error but still the output is an empty matrix.
I would deeply appreciate ANY help to get me started as I'm getting quite frustrated. Also I#d be real happy if you could recommend any literature that would help in my case.
R version 3.5.3 (2019-03-11) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LCCOLLATE=GermanGermany.1252 LCCTYPE=GermanGermany.1252
[3] LCMONETARY=GermanGermany.1252 LCNUMERIC=C
[5] LCTIME=German_Germany.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] affy1.60.0 GEOquery2.48.0
[3] beadarray2.32.0 limma3.36.5
[5] BiocInstaller1.30.0 illuminaHumanv1.db1.26.0
[7] illuminaHumanv2.db1.26.0 org.Hs.eg.db3.7.0
[9] AnnotationDbi1.44.0 IRanges2.16.0
[11] S4Vectors0.20.1 ggplot23.1.0.9000
[13] Biobase2.42.0 BiocGenerics0.28.0
