Question: Problem in RMA normalization (Microarray Affymetrix)
gravatar for Microuser
7 months ago by
Microuser0 wrote:


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?):

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
Calculating Expression
**Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] 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?

Thanks :)

affybatch microarray oligo rma • 230 views
ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 7 months ago by Microuser0

I would download the data and process it manually.

ADD REPLYlink written 7 months ago by Kevin Blighe71k
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