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Question: Normalization of Illumina Microarray Data
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gravatar for paul.elliot1994
8 months ago by
paul.elliot19940 wrote:

If it's not too much Trouble, can someone tell me as to how do I, read in the txt file in R studio? The Raw data was downloaded from GEO. The data accession number is GSE48624.

Moreover, how do i Differentiate the control sample from the normal sample since there are only txt files available in the raw data compressed file!

Thank you very much!

 

ADD COMMENTlink modified 8 months ago by Gordon Smyth32k • written 8 months ago by paul.elliot19940
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gravatar for Mark Dunning
8 months ago by
Mark Dunning1.0k
Cancer Research Uk Cambridge Institute, Cambridge (until October 2017)
Mark Dunning1.0k wrote:

The "raw data" for this dataset seem to be the annotation files for the arrays, and not the raw intensities at all. So not helpful for analysis.

However, you can use the GEOquery package to import the normalised intensities

library(GEOquery)
remotefile <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48624/matrix/GSE48624_series_matrix.txt.gz"

destfile <- "GSE48624_series_matrix.txt.gz"
if(!file.exists(destfile)) download.file(remotefile, destfile)
mydata<- getGEO(filename=destfile)

Phenotypical data can be obtained using the pData function

pd <- pData(mydata)

pd

The vector pd$source_name_ch1 will tell you whether each sample was in the before or after group

pd$source_name_ch1

The function exprs will extract the normalised values

exprs(mydata)

Hope this helps,

ADD COMMENTlink modified 8 months ago • written 8 months ago by Mark Dunning1.0k

Thank You so much Mark, For helping me out. God bless!

ADD REPLYlink written 8 months ago by paul.elliot19940

If it's not too much trouble, can you tell me as to how to perform differential expression analysis on the same and get the list of upregulated and downregulated genes using the same Dataset(GSE48624)Thank You !

ADD REPLYlink written 8 months ago by paul.elliot19940
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