Question: How to convert dataframe into ExpressionSetIllumina / summarized data with beadarray package?
0
gravatar for salamandra
13 days ago by
salamandra0
salamandra0 wrote:

In documentation (beadsummary.pdf) of beadarray package it explains how to get a ExpressionSetIllumina from data deposited on GEO. Something like:

library(GEOquery)
url <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE33126/"
filenm <- "GSE33126_series_matrix.txt.gz"
if(!file.exists("GSE33126_series_matrix.txt.gz")) download.file(paste(url, filenm, sep=""), paste0(getwd(),'/',filenm))
gse <- getGEO(filename=filenm)
# Convert into ExpresssionSetIllumina:
summaryData <- as(gse, "ExpressionSetIllumina")
summaryData

However, this is already normalized data. It also explains how to get "ExpressionSetIllumina" from IDAT files, but the raw data I am trying to get is not idat file, as you see in suppl. files of following studies: GSE22247 GSE26677

I can get those supplementary txt files with:

dataRAW <- read.delim(paste0(txtpath), sep='\t', skip = 4, header = T)

How can I convert dataframe (dataRAW) into an ExpressionSetIllumina object ?

p.s: I need raw data to test different normalisations and latter do dif. gene expression analysis.

beadarray • 43 views
ADD COMMENTlink modified 13 days ago by Mark Dunning1.1k • written 13 days ago by salamandra0
Answer: How to convert dataframe into ExpressionSetIllumina / summarized data with beada
3
gravatar for Mark Dunning
13 days ago by
Mark Dunning1.1k
Sheffield, Uk
Mark Dunning1.1k wrote:

I would probably start by reading these data using limma

data <- limma::read.ilmn("GSE22247_non-normalized_data.txt",expr = "SAMPLE")

and then following steps from the limma user guide for normalisation

ADD COMMENTlink written 13 days ago by Mark Dunning1.1k
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