Differential Expression of c.diff. microarray
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SSK ▴ 10
@ssk-7679
Last seen 5.9 years ago
United Kingdom

Hello,

I am interested in determining the differential expression in E-GEOD-37442. Does anyone know of some code that I can adapt to the analysis of this array. In the array description it says A-GEOD-15470 - Agilent-024835 CDv2_0_1 [ProbeName version] 

Thank you so much!

arrayexpress differential expression • 719 views
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@james-w-macdonald-5106
Last seen 20 hours ago
United States

Sure. There is a metric ton of code in the limma User's guide that you could adapt.

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SSK ▴ 10
@ssk-7679
Last seen 5.9 years ago
United Kingdom

 

I have read the manual for Limma but I am not sure of the specifications for E-GEOD-37442. I have the following line of code:

SDRF <- read.delim("E-GEOD-37442.sdrf.txt",check.names=FALSE,stringsAsFactors=FALSE)

but i am not sure what are the specifications for read.maimages? I have this line for the Limma manual but I am not sure how I can adapt it for E-GEOD-37442.

x <- read.maimages(SDRF[,"Array Data File"],source="agilent",green.only=TRUE)

Also, would you know if there are microarray analysis services provided somewhere? I am worried I can't learn all of the tools within a reasonable time frame.

 

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Yes. There are microarray analysis services provided lots of places. Did you try a google search?

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