Question: How to make lumi accept .txt data?
gravatar for Kristin Muench
5.5 years ago by
United States
Kristin Muench540 wrote:


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:

testMat <- as.matrix(GSE_data)
testMat <- testMat[,-1] # to get rid of probe IDs in first column

# 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 • 2.7k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Kristin Muench540
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2176 users visited in the last hour