Error while normalizing [miRNA-1_0] Affymetrix miRNA Array cel files
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@arisarkar88-11464
Last seen 4 days ago
Los Angeles

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

microrna microarray cdfinfo • 860 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

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.

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Thank you for the reply. It helped. I have 7 cel files and this is what I get on running the command suggested by you:

miRNA-1_0 miRNA-1_0_2Xgain
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So, can you please help me in this regard? How can I normalize these two array types together and carry the analysis for obtaining the differentially expressed miRNAs? I wonder how these files can be different as they belong to the same experiment? Please suggest.

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I have never even heard of these 2Xgain arrays, and I don't see anything obvious on Affy's site. You will probably need to talk to whomever you got these data from (or if they are from your lab, your Affy rep) to find out what the deal is.

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Ok..I will check it out.