I have some normalized microarray data in an object generated by the following commands:
> raw_data5 <- oligo::read.celfiles(filenames = "VV51m.CEL", "VV50m.CEL", ...) > pd3 <-read.AnnotatedDataFrame("factors_all.txt",header=TRUE,sep="\t") > rownames(pd3) <- pd3$Array > phenoData(raw_data5) <- pd3
I normalized using rma:
> my_eset_norm <- oligo::rma(raw_data5) > exp_my <- Biobase::exprs(my_eset_norm)
This now contains all probe data from the .cel files. I would like to extract just the miRNA probes from the normalized object. I have tried the following command, taken from a thread whose user reportedly executed this successfully:
> miRNA_probenames.tb <- read.table("miRNAprobes.txt") > miRNAprobes <- miRNA_probenames.tb$V1 > my_eset_norm_just_miRNA <- exprs(my_eset_norm)[miRNAprobes, ]
However, when I do it, the probes in my_eset_norm_just_miRNA are not the ones contained in the miRNAprobes object (which is nothing but a list of probe IDs:
> miRNAprobes  hsa-let-7a-2-3p hsa-let-7a-3p hsa-let-7a-5p hsa-let-7b-3p  hsa-let-7b-5p hsa-let-7c-3p
Does anyone know what I am doing wrong here, or can you suggest the appropriate command to extract a subset of my_eset_norm for just the desired probes?
I'd appreciate any help you can offer!