Question: Analyzing Agilent custom array in R
0
2.5 years ago by
arisarkar880 wrote:

How to analyze datasets corresponding to 'Agilent-016332 Human Gene Expression 8X15k (AMADID: 16332)' in R?

agilent microarrays analyze • 1.1k views
modified 2.5 years ago by James W. MacDonald51k • written 2.5 years ago by arisarkar880
Answer: Analyzing Agilent custom array in R
0
2.5 years ago by
United States
James W. MacDonald51k wrote:

You would most likely want to use limma. Using the only GEO data set for this array as an example:

> library(GEOquery)

> getGEOSuppFiles("GSE72246")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72246/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72246/suppl//GSE72246_RAW.tar'
Content type 'application/x-tar' length 142499840 bytes (135.9 MB)

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72246/suppl//filelist.txt'
Content type 'text/plain' length 3621 bytes
> setwd("GSE72246/")
> untar("GSE72246_RAW.tar")

> dat <- read.maimages(dir(".", "txt.gz"), "agilent.median", green.only = TRUE)
>

And now you can make whatever comparisons you might like. The limma User's Guide has examples of reading in this sort of data on p. 19, and a worked example starting on p. 110. But after the normalization step, a single color Agilent analysis isn't materially different from any of the Affy examples, and you could use one or more of those as an example since the Agilent example is a time course.

Thank you for the reply. It was really helpful. I checked the user guide for limma. Therein Quantile normalization has been used. Is it possible to use '75th percentile/upper quartile' normalization using limma?