Question: Error while normalizing [miRNA-1_0] Affymetrix miRNA Array cel files
0
gravatar for arisarkar88
2.9 years ago by
arisarkar880 wrote:

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

microarray microrna cdfinfo • 585 views
ADD COMMENTlink modified 2.9 years ago by James W. MacDonald50k • written 2.9 years ago by arisarkar880
Answer: Error while normalizing [miRNA-1_0] Affymetrix miRNA Array cel files
0
gravatar for James W. MacDonald
2.9 years ago by
United States
James W. MacDonald50k wrote:

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.

ADD COMMENTlink written 2.9 years ago by James W. MacDonald50k

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:

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

       miRNA-1_0 miRNA-1_0_2Xgain 
               3                4

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.

ADD REPLYlink written 2.9 years ago by arisarkar880

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.
 

ADD REPLYlink written 2.9 years ago by James W. MacDonald50k

Ok..I will check it out.

ADD REPLYlink written 2.9 years ago by arisarkar880
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 16.09
Traffic: 145 users visited in the last hour