[BioC] From GEO to aCGH and snapCGH

[Sean Davis]

João Fadista wrote:
> Dear Sean Davis,
>
> I already put the Position and Chromosome elements in the $genes dataframe.
> So then I tried again the function processCGH, but it gave me this error:
>
>   
>> MA5 <- processCGH(MA4, method.of.averaging = mean, ID="ID")
>>     
> Processing chromosome  1 
> Processing chromosome  10 
> Processing chromosome  11 
> Processing chromosome  12 
> Processing chromosome  13 
> Processing chromosome  14 
> Processing chromosome  15 
> Processing chromosome  16 
> Processing chromosome  17 
> Processing chromosome  18 
> Processing chromosome  19 
> Processing chromosome  2 
> Processing chromosome  20 
> Processing chromosome  21 
> Processing chromosome  22 
> Error in if (kb >= chrominfo$centromere[chr]) median(vec[clones.info$Chr ==  : 
>         missing value where TRUE/FALSE needed
>
> Do you have any idea of what could be wrong? Thanks again for helping me.
>
>   
It appears that you are making progress, Joao.  Just for future 
reference, when you reply to messages from an email list, it is best to 
reply to the list so that everyone can learn from the discussion and so 
that you get the best advice possible.  In this case, I'm not sure what 
is causing your error, but others on the list likely do know what the 
problem is and most likely have a solution for you.

Sean

> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
> Sent: 26 November 2006 02:41
> To: João Fadista; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] From GEO to aCGH and snapCGH
>
> João Fadista wrote:
>   
>> Hi,
>>
>> Thanks for the tip.
>> I already have the chromosome and the position of the gene entrez ids. Do you know how can I substitute in my MAList the MA$genes$Entrez.GeneID with both the columns Position and Chr?
>>   
>>     
>
> That's great.  You can use the merge() function to join the MA$genes data frame with the data frame that contains the Entrez Gene ID and associated Position and Chromosome. 
>
> Sean
>