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Question: problems loading imagene data with limma
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gravatar for Ingunn Berget
8.5 years ago by
Ingunn Berget150
Ingunn Berget150 wrote:
Hello all I want to load imagene data with limma and have encountered problems I have used the following command to read the data, and get an error: > RG <- read.imagene(files, columns = list( f="Signal Mean",b ="Background Mean"), path=rawdata) Read header information Read H:/Prosjekter/ExpressionSalmon/pilotstudyHanna/Rawdata/JA005_2498 Cy3.txt Error in RG$G[, i] <- obj[, columns$f] : number of items to replace is not a multiple of replacement length files: data frame with file names for the rawdata, 10 rows and 2 columns, one column for the Cy3 and one for the Cy5 files rawdata: String which defines the path I have tried different solutions that I have found in the mailing archives, but they did not help. Finally I discovered one column in the raw data control called "control" which were empty for all rows in the file I checked. I tried to delete this column in both of the raw data files for this array, and Used files2 <- c("testCy3","testCy5") RG <- read.imagene(files2, columns = list( f="Signal Mean",b ="Background Mean"), path=rawdata) This worked well for the array I tried it on (testCy3 and testCy5 are the modified rawdata files) Now I can of course do this for all arrays, but modifying 20 files is boring and in the next experiment there will more arrays. Question 1: Anybody who knows how I can solve this problem more elegantly? Question 2: What is this "control" column in the Imagene files? Best regards Ingunn Berget (Dr. Scient) UMB, box 5003, IHA 1432 ?s Norway Centre for Integrative Genetics, www.cigene.no Centre for Biospectroscopy and Data Modelling, www.specmod.org
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