I am trying to continue microarray analysis and still have got some problems. I managed to download an Array Express file with 22 CEL files in. Because I was only interested in 6 of them, I removed the other 16 manually.
Downloading the raw data from ArrayExpress (initially used to get the whole CEL files and other files):
anno_AE <- getAE("E-GEOD-15936", path = raw_data_dir , type = "raw") sdrf_location <- file.path(raw_data_dir, "E-GEOD-15936.sdrf.txt") SDRF <- read.delim(sdrf_location) rownames(SDRF) <- SDRF$Array.Data.File SDRF <- AnnotatedDataFrame(SDRF)
Then, I used these codes to link phenodata to my raw reads using affy (I don't know how better I could do it because I got unreadble CEL file error?):
library(affy) celFiles <- list.celfiles() raw_data <- read.affybatch (celFiles, verbose = FALSE, phenoData = SDRF) **Warning message: In read.affybatch(celFiles, verbose = FALSE, phenoData = SDRF) : Incompatible phenoData object. Created a new one.** phenoData(raw_data) <- SDRF annotation(raw_data) <- "pd.yeast.2" palmieri_eset <- rma(raw_data, target = "core")
But, I get the error:
Background correcting Normalizing Calculating Expression **Error in dimnames(x) <- dn : length of 'dimnames'  not equal to array extent**
I don't know why. Anyone can help suggest me ways to modify my code? I suspect that might be because I removed some CEL files?