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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)
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gravatar for hks04180
4 months ago by
hks041800
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:

GSE17856_RAW.tar   

GSE17856_Readme.txt                                                

GSE17856_US14702406_251485032844_S01_GE2-v5_91_0806_1_1.txt                                

GSE17856_US14702406_251485032848_S01_GE2-v5_91_0806_1_4.txt

GSE17856_US14702406_251485014865_S01_GE2-v5_91_0806_1_1.txt

GSE17856_US14702406_251485032849_S01_GE2-v5_91_0806_1_1.txt

GSE17856_US14702406_251485014870_S01_GE2-v5_91_0806_1_4.txt

GSE17856_US14702406_251485032878_S01_GE2-v5_91_0806_1_1.txt

GSE17856_US14702406_251485028288_S01_GE2-v5_91_0806_1_1.txt

GSE17856_US14702406_251485032882_S01_GE2-v5_91_0806_1_4.txt

 

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

 

 

Thank you!

ADD COMMENTlink modified 4 months ago by James W. MacDonald48k • written 4 months ago by hks041800
1
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald48k 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 4 months ago by James W. MacDonald48k

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

ADD REPLYlink written 4 months ago by hks041800
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