Microarray Analysis Trouble in Analysis

Very Dificult follow the Microarray Analysis tutorial.

I treid to follow, tutorials of Micoarray Analysis

it went smoothly upto Data import and processing, .. But in Expression anlaysis i am not able to generate the file DataMatrix objects. I feel there are some commonds are missing in Processing..

If any one had idea please help on this.

[Arthur Goldsipe]

You didn't give us enough information to be able to help you. Can you provide us with more details?

• What tutorial are you trying to do? Can you provide us with a link to the tutorial? Or at least the title of the tutorial?
• What went wrong? What command did you run? What error message did you get?

[Babajan Banaganapalli]

Thank you so much for you replay.

Here the steps I DID

Step 1: (Preprocessing Affymetrix® Microarray Data at the Probe Level)

I have .CEL files, I Uploaded and process them using the below example

https://uk.mathworks.com/help/bioinfo/examples/preprocessing-affymetrix-microarray-data-at-the-probe-level.html

I successfully generate the all the files in above example

Step: 2 (Exploring Microarray Gene Expression Data)

Struck this step, I don’t know how to generate MAT file expression containing three DataMatrix objects (expr_rma, rma_mle, gcrma_eb) associated with the gene expression values.

https://uk.mathworks.com/help/bioinfo/examples/exploring-microarray-gene-expression-data.html

Please let me know, how I can generate DATA matrix object, to process further in the analysis.

Thank You

Answer 1

[Arthur Goldsipe]

Let me make sure I understand your problem. You are trying to run the following example:

https://uk.mathworks.com/help/bioinfo/examples/exploring-microarray-gene-expression-data.html

However, you do not know how to create the DataMatrix objects.

If you just want to run the example as written, you don't need to construct your own DataMatrix objects. You can just load them from the example file by running the command load cnsexpressiondata. But I assume you want to modify the example by using your own data, and so you'd like to put that data in DataMatrix objects. If that's your goal, then I recommend exploring the following example to see if it teaches you how to create your own DataMatrix objects:

https://www.mathworks.com/help/bioinfo/ug/representing-expression-data-values-in-datamatrix-objects.html