[BioC] illegal operand when I run DEXSeq

[Steve Lianoglou]

Hi,

I just wanted to ensure that you were using the latest version of the
DEXSeq package, which you are.

I'm not sure what other help I can offer other than the suggestion
that it seems like it's time to do a bit more in depth debugging on
your part, which won't be too easy if you're not comfortable with
doing these types of things.

>From your original output, it seems like the problem must be somewhere
in the top 100 genes being tested, since there wasn't a "." printed to
the console (I think it prints that every ~ 100 genes to keep you
informed of it's progress).

Perhaps you can see if it works when you exclude the top 100 genes,
and debug backwards from there?

Digging into the estimateDispersions function and having it print to
the console the name of each gene as it is estimating dispersions
would be another idea.

All of this is assuming that your input data is sane, which we have no
way to verify from our end. Are the `counts()` of your ExonCountSet
sane, for starters?

-steve

On Wed, Feb 27, 2013 at 4:40 PM, Ou, Jianhong <Jianhong.Ou at umassmed.edu> wrote:
> Hi Steve,
>
> Because R is crashed after I run the code, I can only show you my sessionInfo before that.
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DEXSeq_1.4.0        Biobase_2.18.0      BiocGenerics_0.4.0
> [4] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] biomaRt_2.14.0 hwriter_1.3    RCurl_1.95-3   statmod_1.4.16 stringr_0.6.2
> [6] tools_2.15.2   XML_3.95-0.1
>
>
> Yours sincerely,
>
> Jianhong Ou
>
> jianhong.ou at umassmed.edu
>
>
> On Feb 27, 2013, at 4:32 PM, Steve Lianoglou wrote:
>
>> Hi,
>>
>> On Wed, Feb 27, 2013 at 4:04 PM, Ou, Jianhong <Jianhong.Ou at umassmed.edu> wrote:
>>> Hi All,
>>>
>>> I got illegal operation when I run DEXSeq.
>>>
>>> May I know the possible reasons for this error?
>>
>> Can you show the output of `sessionInfo()` after you load DEXSeq so we
>> can see the package versions you are using?
>>
>> (also, please be more prudent in the size of the "log" you paste into
>> the email you send to the list ... having a list of all of the genes
>> in your study is a bit much ;-)
>>
>> -steve
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact