How can I read the MMIntensities from CEL files using celintensityread()?

I read in several CEL-files and the corresponding CDF file using celintensityread:

CEL_files_wCDF = celintensityread(CEL_files, path_CDF_file, 'CELPath', path_CEL_files);

When I'm looking at my "CEL_files_wCDF" variable, I can only find the PMIntensities, but not the MMIntensities. The CDF file should contain their position as I checked for it by using the following commands:

cdfStruct = affyread(CDF_file_name, path_CDF_file);
cdfStruct.ProbeSetColumnNames
cdfStruct.ProbeSets(index).ProbePairs

How can I retrieve the information about the MMIntensities using celintensityread()?

Thanks a lot in advance for any help.

Edit:

You can find the CEL-files here:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11906 (look for GSE11906_RAW.tar)

The CDF-file can be found here:

http://www.affymetrix.com/support/technical/byproduct.affx?product=hg-u133-plus (under "Library files")

[Luuk van Oosten]

Dear Fabienne,

Can you attach (a couple of) the CEL file(s) you are trying to open, so one can try out whatever it is that you are trying to do?

Thanks in advance.

[Fabienne Rössler]

Dear Luuk,

Unfortunately, the CEL-files are too big to attach them to my question (even after compression). But I added a link to the CEL-files and also the CDF-file to my original question. I hope this helps.

Answer 1

[Chidvi Modala]

ProbeStructure = celintensityread(..., 'PMOnly', PMOnlyValue, ...) includes or excludes the mismatch (MM) probe intensity values. When PMOnlyValue is true, celintensityread returns only perfect match (PM) probe intensities. When PMOnlyValue is false, celintensityread returns both PM and MM probe intensities. Default is true.

You can refer to https://www.mathworks.com/help/bioinfo/ref/celintensityread.html

[Fabienne Rössler]

Thank you so much, I totally overlooked this input argument.