extracting a subset of probes from an expression object

Question

[RNAseqer]

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
   [1] hsa-let-7a-2-3p    hsa-let-7a-3p      hsa-let-7a-5p      hsa-let-7b-3p     
   [5] 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!

[Sean Davis]

Your code looks OK. What are the dimensions of my_eset_norm_just_miRNA?