I have one question that needs your help. Suppose that I need to process GSE39340 data set.
M1. I used GEOquery to get the data and normalized it by the below commands:
library(GEOquery) library(lumi) eset <- getGEO("GSE39340") lumi.N.Q <- lumiExpresso(eset$GSE39340_series_matrix.txt.gz, normalize.param = list(method='rsn')) write.exprs(lumi.N.Q, file = 'processedExampledata.txt')
M2. I don't use GEOquery but instead downloaded the txt file directly from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39340) and processed using the same method described below:
example.lumi <- lumiR("GSE39340_non_normalized.txt") lumi.A.B <- lumiExpresso(example.lumi, normalize.param = list(method='rsn')) write.exprs(lumi.A.B, file = 'processedExampledata1.txt')
However, when comparing the output files, the expression values of the same probe/sample are quite different. For example, ILMN_1343295 of GSM966273 (aka E31) were 11.67 vs 11.80 in processedExampledata and processedExampledata1, respectively. I don't know why.
Please let me know where I get lost.