Dear Bioconductor Community,
i recently aquired 3 txt files from a microarray experiment including Illumina Human HT-12 v4 beadchip and i used the lumi package and vignette to preprossess the data in the following way
rawdata <- "SampleProbeProfile_Dimitra3.txt" # includes columns refering to PROBE_ID, AVG_Signal,..
smplfile <- "SampleTableControl_Dimitra3.txt # phenoData information about the samples and the Groups
ctrlprobes <- "ControlProbeProfile_Dimitra3.txt" # information about the control probes
lib_mapping <- "lumiHumanIDMapping"
rawdata.lumi <- lumiR.batch(rawdata, lib.mapping=lib_mapping, sampleInfoFile= smplfile)
Inputting the data ...
Adding nuID to the data ...
Loading required package: lumiHumanIDMapping
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:simpleaffy’:
members
Loading required package: DBI
No Quality Control assessment of the object because it is not a "LumiBatch" object.
rawdata.lumi <- addControlData2lumi(ctrlprobes, rawdata.lumi)
Inputting the data ...
Error in checkAtAssignment("ExpressionSet", "controlData", "data.frame") :
‘controlData’ is not a slot in class “ExpressionSet”
class(rawdata.lumi)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
also i tried lumi.T <- lumiT(rawdata.lumi) but
Error in lumiT(rawdata.lumi) : Slot se.exprs is required!
Any ideas or help ??
Furthermore, i have found from limma a way of preprocessing illumina raw data, but i dont know which method (including normalization and background correction) is more effective and superior for illumina data
Hi user svlachavas
I am new to this analysis and would like your valuable suggestions to process my data. If its fine for you, kindly contact me on mathew.mano@gmail.com