help regarding loading text files in affy package for background correction
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7 months ago
raavi21198 ▴ 10

Hi all, I have to do perform background correction of an miRNA dataset which has RAW data in GEO. I have downloaded all the files. I need help to perform background correction for these .txt files and perform normalisation and Differential gene expression using limma. My major doubt is can do you need CEL files for background correction or can text files be used?? Below is my code (GSE ID is GSE59973) Please help me figure out this

library(Biobase) library(GEOquery) library(limma) gset <- getGEO("GSE59973", GSEMatrix =TRUE, AnnotGPL=FALSE) if (length(gset) > 1) idx <- grep("GPL16770", attr(gset, "names"))else idx <- 1 gset <- gset[[idx]] View(gset) library(affy) list.files() readdata <- ReadAffy(filenames="GSM1462895_US10313827_253118111239_S01_miRNA_107_Sep09_1_1.txt.gz","GSM1462896_US10313827_253118111239_S01_miRNA_107_Sep09_1_2.txt.gz","GSM1462897_US10313827_253118111239_S01_miRNA_107_Sep09_1_3.txt.gz","GSM1462898_US10313827_253118111239_S01_miRNA_107_Sep09_2_1.txt.gz","GSM1462899_US10313827_253118111239_S01_miRNA_107_Sep09_2_2.txt.gz","GSM1462900_US10313827_253118111239_S01_miRNA_107_Sep09_2_3.txt.gz")

R affy textfiles • 211 views

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