Error while using justRMA() for microRNA array files of platform [miRNA-1_0] Affymetrix miRNA Array

Error in read.celfile.probeintensity.matrices(filenames = filenames, cdfInfo = cdfInfo,  : 
 .CEL does not seem to be of miRNA-1_0_2Xgain type

Can somebody help solve this problem? Really stuck with this.

Regards

That error comes up when you have a mixture of different array types that you are trying to read in together. The function that reads in the data looks at the first file to see what type of array it was, and then each successive file has to have come from that same array type. Evidently the first one you read in was a miRNA-1_0_2Xgain, and then you tried to read in a file that was not of that type, hence the error.

You can get a listing of the types of files you have using read.celfile.header in the affyio package (or alternatively the readCelHeader function in affxparser)
 

> fls <- dir(".", "CEL$")

> fls
 [1] "MKE_L10.CEL" "MKE_L11.CEL" "MKE_L12.CEL" "MKE_L13.CEL" "MKE_L14.CEL"
 [6] "MKE_L15.CEL" "MKE_L18.CEL" "MKE_L1.CEL"  "MKE_L20.CEL" "MKE_L21.CEL"
[11] "MKE_L24.CEL" "MKE_L29.CEL" "MKE_L2.CEL"  "MKE_L30.CEL" "MKE_L33.CEL"
[16] "MKE_L34.CEL" "MKE_L38.CEL" "MKE_L40.CEL" "MKE_L41.CEL" "MKE_L43.CEL"
[21] "MKE_L45.CEL" "MKE_L46.CEL" "MKE_L47.CEL" "MKE_L49.CEL" "MKE_L50.CEL"
[26] "MKE_L51.CEL" "MKE_L5.CEL"  "MKE_L6.CEL"  "MKE_L7.CEL"  "MKE_L8.CEL"

> table(sapply(fls, function(x) read.celfile.header(x)$cdfName))

miRNA-3_0
       30

So I have 30 celfiles in that directory, and all of them are miRNA-3_0. If you do the same, you will most likely get a table with more than one celfile type.