Jo?o Fadista wrote:
> Hi,
>
> Does anyone knows how can I convert the format from a GEO (Gene
Expression Omnibus) CGH dataset to a format suitable to be analysed by
the snapCGH and aCGH packages?
>
Joao,
What is the GEO accession number? Does the platform information
include
a chromosome and location for the probes? What have you tried and
what
hasn't worked?
Sean
Jo?o 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
Jo?o 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$Chr == :
> missing value where TRUE/FALSE needed
>
> Do you have any idea of what could be wrong? Thanks again for
helping me.
>
>
It appears that you are making progress, Joao. Just for future
reference, when you reply to messages from an email list, it is best
to
reply to the list so that everyone can learn from the discussion and
so
that you get the best advice possible. In this case, I'm not sure
what
is causing your error, but others on the list likely do know what the
problem is and most likely have a solution for you.
Sean
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: 26 November 2006 02:41
> To: Jo?o Fadista; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] From GEO to aCGH and snapCGH
>
> Jo?o Fadista wrote:
>
>> Hi,
>>
>> Thanks for the tip.
>> I already have the chromosome and the position of the gene entrez
ids. Do you know how can I substitute in my MAList the
MA$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
>
