Question: Using PAcalls for Clariom chips
gravatar for kmvaldez2
3.0 years ago by
kmvaldez210 wrote:

Has anyone had luck using the PAcalls() function of bioconductor with Clariom arrays? I am able to use it successfully with HG U133 (using "MAS5") and (using "PSDABG"), but my Clariom S Human array give me the error "Subscript out of bounds". All of the data is processed the same way before attempting to do the present absent calls.

Below is an example of my code:

These work:

result = paCalls(HG133data, "MAS5")
result = paCalls(hugeneData, "PSDABG")

This however gives the error "Warning: Error in [: subscript out of bounds"

result = paCalls(ClariomShumanData, "MAS5")

My guess is that the paCalls function does not work with this smaller chip, prompting the error. But any insight or work-arounds are much appreciated.

Thanks, Kris

microarray bioconductor R • 952 views
ADD COMMENTlink modified 3.0 years ago by WouterDeCoster44k • written 3.0 years ago by kmvaldez210

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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ADD REPLYlink written 3.0 years ago by WouterDeCoster44k

Hi Kris:

Did you ever get a solution to this? I'm having similar issues with the Clariom D mouse array.

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘paCalls’ for signature ‘"HTAFeatureSet"’
ADD REPLYlink written 2.7 years ago by Gareth Palidwor1.6k
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