Question: How to make lumi accept .txt data?
0
gravatar for Kristin Muench
4.2 years ago by
United States
Kristin Muench450 wrote:

Hello,

I am trying to do background correction/ quantile normalization on a .txt file of expression values (.CEL data is unavailable to me). GSE_data is a 47,000 x 73 dataframe with headers of expression values. The data was gathered on an Illumina microarray.

I'm trying to use lumi like so:

library(lumi)
testMat <- as.matrix(GSE_data)
testMat <- testMat[,-1] # to get rid of probe IDs in first column
eset<-new("ExpressionSet",exprs=testMat)

# background correction/RMA normalization
lumiObj <- lumiB(eset, method='bgAdjust',verbose=TRUE)

 

But I get this error:

error in evaluating the argument 'object' in selecting a method for function 'exprs': Error in bgAdjust(x.lumi, ...) : The object should be class "LumiBatch"!

Can anyone see what I'm doing wrong? What's the best way to do background correction/quantile normalization on .txt data?

Thank you so much!

 

EDIT: When I rewrite the eset definition as:

eset<-new('LumiBatch', exprs = test)

I then get the error:

Error in `featureNames<-`(`*tmp*`, value = c("1", "2", "3", "4", "5",  : 
  'value' length (47308) must equal feature number in AssayData (47308)

 

EDIT 2: Also, using lumiR doesn't seem to work - inputting this (importme = file in my path that is a .txt file of the expression values only)

try.lumi <- lumiR('importme')

I get this:

Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi microarray • 2.1k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Kristin Muench450
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