Hi Martin,


I have figured out that the atomic error was due to having a different number of replicates at each time point.


Best regards,


Anthony Bosco


From: Martin Aryee <aryee@jhu.edu>
To: bioconductor@stat.math.ethz.ch
Cc: abosco@arc.arizona.edu
Sent: Sat, 13 February, 2010 4:24:39 PM
Subject: Re: [BioC] is.atomic error with betr function

> Date: Thu, 11 Feb 2010 17:33:15 -0700
> From: "Anthony Bosco" <abosco@arc.arizona.edu>
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC]  is.atomic error with betr function
> Message-ID:
>        <6V8SzW2U.1265934795.4953820.abosco@respiratory.arizona.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear list,
>
>
> I am having trouble using the function betr (BioC package betr)..
>
> I am providing the required arguments (cond, timepoint, replicate) in the
> correct length and class, as well as a data matrix (exprs).
>
> However I get the following error
>
> Error: is.atomic(x) is not TRUE
>
> This occurs even though is.atomic(exprs) = TRUE
>
> I also get the following warnings...
>
>> warnings()
> Warning messages:
> 1: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 2: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 3: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 4: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 5: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 6: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 7: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 8: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 9: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 10: In mean.default(newX[, i], ...) :
>  argument is not numeric or logical: returning NA
> 11: In mean.default(newX[, i], ...) :
>

Hi Anthony,

Are you able to construct a minimal example that shows the contents of
the input variables and recreates the error? It would be easier to
debug if I could see the actual values being used.

Martin.

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