Hi, I am super strugling with Agilent two colour microarray. I am moving forward, but super slowly. Now I am in the possession of a decent script where i have to upload Spottype file. All the files for this array I finally found but when i upload spottype file i get an error.
So what I see is below.
data=read.maimages(files = target, source ="agilent", green.only = F, columns = list(G="gMedianSignal",Gb="gBGMedianSignal",R="rMedianSignal",Rb="rBGMedianSignal"),
annotation = c("ProbeName","SystematicName") )
plotMD(object = data) spottypes=readSpotTypes(file = "Spots3.txt", check.names=FALSE)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 32133 did not have 20 elements
I even tried to delete this line but the error cames up all the time. Can someone please help me? Maybe I am uploading wrong file time as this Spottype file?
Is this your or published data? This all seems overly complicated to me. Just read the CEL files into R and normalize with RMA as suggested in the limma manual.
This is my data but the script was given to me by someone else. Could you share with me the code to do it or limma manual?
Ok, but what data do you have? CEL files?
txt files I have, Thanks ATpoint, I have followed this limma guidelines and finally start to understand My txt files starts with something like that
CEL files are an Affymetrix format they and are only produced by Affy arrays. Agilent arrays have spots in instead of probe-sets. The Agilent Feature Extraction software produces text files in the format shown by OP, which are read by