How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
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kanacska ▴ 10
@kanacska-7375
Last seen 6.1 years ago
Hungary

Hi,

Im doing annotation on this article: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38376

Ive read in the txt file in R studio, but i dont know how to normalize it.

Thanks,

 

Anna

illumina normalization microarray • 2.6k views
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If it's not too much trouble can you tell me as to how did you read in the txt file in R studio? Thank you!

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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 16 days ago
Sheffield, Uk

Not sure which text file you are referring to, but if you just want to have a look at the data and start exploring it, the easiest thing would be to load it using GEOquery.

library(GEOquery)

data <- getGEO("GSE38376")[[1]]

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kanacska ▴ 10
@kanacska-7375
Last seen 6.1 years ago
Hungary

Thank you. This one on the page: GSE38376_non-normalized.txt

I want to do a QC and to get a gene list of diferencialy expressed genes

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kanacska ▴ 10
@kanacska-7375
Last seen 6.1 years ago
Hungary

but ive never used illumina just affymetrix

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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 16 days ago
Sheffield, Uk

I'm pretty sure that file isn't in the standard format exported by Illumina's software. Usually you expect to see columns with the prefix AVG_Signal. The following is a bit of a hack, but will give you an object to play around with;

 

library(limma)

idata <- read.ilmn("GSE38376_non-normalized.txt",probeid = "PROBE_ID",expr="SKBR")

 

The limma user guide has examples of processing Illumina data and doing differential expression with these kinds of objects.

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Dear Mark,

Sorry to bother you but if you can take a look at my post and can give me any suggestion, should be helpful. https://support.bioconductor.org/p/125225/

Thank you,

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