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

Fabienne Rössler さんによって質問されました 2019 年 8 月 6 日

最新アクティビティ Fabienne Rössler さんによってコメントされました 2019 年 8 月 13 日

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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")

2 件のコメント

Luuk van Oosten 2019 年 8 月 7 日

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 2019 年 8 月 7 日

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.

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回答者: Chidvi Modala 2019 年 8 月 13 日

採用された回答

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

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Fabienne Rössler 2019 年 8 月 13 日

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

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R2018b

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Fabienne Rössler (view profile)