Question: Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from GEO raw data (Agilent array data)
gravatar for hks04180
18 months ago by
hks041800 wrote:

Hello all,

I downloaded the raw data for the Agilent from GEO (), but I do not know how to build the expression matrix step by step. Can anyone of you help me?

Although I have tried limma package for the same.


targetinfo <- readTargets("Targets.txt", sep="\t")

But problem is Targets.txt file is missing in all files.

Some of the files i have download using GeoQuery package are as following:












Next thing where I am confused, which .txt file should be used for preprocessing of raw data.



Thank you!

ADD COMMENTlink modified 18 months ago by James W. MacDonald52k • written 18 months ago by hks041800
Answer: Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent fi
gravatar for James W. MacDonald
18 months ago by
United States
James W. MacDonald52k wrote:

The targets file is often something you need to construct. Examples can be found in section 4.3 of the limma User's Guide.

All of the files (other than the first two) that you list contain raw data. The Readme file (which you should read) contains phenotypic information about the samples hybridized to each array.

As an aside, you cannot expect people on this support site to give you step by step instructions on how you should analyze some data. If you want to be the data analyst, then you have to do so yourself. If you get stuck on something, or have a question we are happy to help. But if you want to be responsible for analyzing some data, you have to take the responsibility, which includes figuring out how to do it yourself. An alternate (and quite valid, I might add) approach would be to find somebody local who knows what they are doing and ask or pay them to do it for you.

ADD COMMENTlink written 18 months ago by James W. MacDonald52k

Thank You James. Yeah most of part I already solved. I was confused with targets.txt file. 

ADD REPLYlink written 18 months ago by hks041800
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