[BioC] bout big data set for Affy R packge

[Benilton Carvalho]

Hi Rob,

looks like you're running an old version of oligo.

Today, our approach is:

library(ff)
library(oligo)
my.data <- read.celfiles(<CEL file names>)

HTH,
b

On 21 December 2012 01:02, Rob Dunne <Rob.Dunne at csiro.au> wrote:
> Hi Wei Liu,
>
> if they are affymetrix 1.0 ST exon arrays, I can send you a modified version of read.celfiles from the oligo package that
> should read a 300 microarray data set. I dont know it it will work for other array types, possibly not without some work.
>  It is a modified version of the read.celfiles that uses the big.matrix class from the big.memory package
>
> my.data<-read.celfiles(filenames=ff,useAffyio=FALSE)
> my. data
> #assayData: 6553600 features, 335 samples
> #Annotation: pd.huex.1.0.st.v2
>
> Bye
> Rob
>
>
>
>
> On 12/20/2012 01:21 AM, 刘伟 wrote:
>> Dear Buddy,
>> I am a user of affy R package. When I attempt to handle a large
>> number (aprox. 300) of microarrays, I always get an error in memory
>> allocation from R. I searched the web but didnot find any solution for
>> readaffy() with large dataset. I donnot know if the problem can be
>> fixed in some way. Any suggestion is appreciated. Thanks.
>>
>> Sincerely,
>> Wei Liu
>>
>>       [[alternative HTML version deleted]]
>>
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>
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