probles with loess normalization in affy
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2.4 years ago
Lila M ★ 1.1k

Hi all, I'm working in published array expression data sets (affymetrix u133b) . I've tried to do some loess normalization but I found some problems. Here the code:

library(affy)
celfiles <- list.files()
rawData <- ReadAffy(filenames =celfiles)
exprs(rawData)
boxplot(rawData)

normData <-normalize.AffyBatch.loess(rawData)
exprs(normData)
boxplot(normData)

So the code compiles properly but when I plot normData the boxplot doesn't look like normalized. Any suggestion? Thanks!

affy microarray loess normalization • 631 views
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Can you show the plot?

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I don't know how to upload the boxplot , but this is a data subset

#raw data
GSM1525198.CEL.gz GSM1525199.CEL.gz GSM1525200.CEL.gz  GSM1525201.CEL.gz
1   403.3   211.0   417.5   310.5
2   16062.0 16321.8 17672.5 13178.8
3   393.8   216.3   372.3   323.8
4   16560.0 16944.3 17771.8 13375.0

#normalized data 
GSM1525198.CEL.gz GSM1525199.CEL.gz  GSM1525200.CEL.gz GSM1525201.CEL.gz
1   373.2181    299.3475    349.5832    282.4489
2   20177.9132  23678.5436  14341.0039  8911.0882
3   363.7140    306.7556    312.7128    294.3092
4   20843.4204  24557.0469  14425.2356  9033.1897
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