ExpressionSet: Internal Standard
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@herbert-meyer-10849
Last seen 5.4 years ago

Hallo,

I am trying to figure out how the ExpressionSet is working. I am new to R and have some problems.

I have a lot of data and want to normalize it with the CRMN package. My data consists of samples and analytes. Some of these analytes are Internal Standards. So with the ExpressionSet I want to provide the data to the normalization functions from the CRMN package.

So I have the samples and the analytes but how do I define which analyt is an Internal Standard? Thats what I have so far:

 

exprsFile <- "C:/Users/..../exprsData.txt"

exprs <- as.matrix(read.table(exprsFile, header=TRUE, sep=",",row.names=1,as.is=TRUE))
class(exprs)
dim(exprs)
colnames(exprs)
head(exprs[,1:5])

minimalSet <- ExpressionSet(assayData=exprs)

 

Isn't there possibility to use the sample in .rda format from the CRMN package and just overwrite it with my data?

 

expressionset • 531 views
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@steve-lianoglou-2771
Last seen 19 hours ago
Denali

I'm not familiar with the CRMN package, so won't answer your specifically, but in general this is type of information you would store in fData(minimalSet).

Among other things, in addition to the matrix of assay values you store in the ExpressionSet, you can store two additional data.frames that provide meta information about the features (rows) of the ExpressionSet (fData) and the columns (samples) (pData) of the ExpressionSet.

I could imagine the fData for your data to include something like "feature_name", "feature_id", and "probe_type" (control or otherwise).

Do you get the general drift?

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