Question: extracting a subset of probes from an expression object
0
gravatar for RNAseqer
18 months ago by
RNAseqer 140
RNAseqer 140 wrote:

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!

subset microarray exprs probes • 385 views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 18 months ago by RNAseqer 140

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

ADD REPLYlink written 15 months ago by Sean Davis26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1605 users visited in the last hour