Question: Problem in RMA normalization (Microarray Affymetrix)
0
gravatar for Microuser
7 months ago by
Microuser0
Microuser0 wrote:

Hi,

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' [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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1997 users visited in the last hour
_