Yuliang,

Yes, you need first run peak calling algorithm such as MACS, the Bioconductor packages chipseq or BayesPeak etc.

If you still encounter memory problem after first running peak calling algorithm, you could try R 64-bit version.

Best regards,

Julie


On 9/17/10 3:14 AM, "Yuliang Tan" <yuliangtan@gmail.com> wrote:

Hi Julie,

I followed the examples in R console, it reported an Error: cannot allocate vector of size 128.0 Mb, my bed file maybe too big, here is the head of this test.bed:

chr8    119445843    119446142    Neg1    1    -    119445843    119446142    153,255,153
chrY    2788549    2788848    Pos2    1    +    2788549    2788848    153,153,255
chr3    53798783    53799082    Neg3    1    -    53798783    53799082    153,255,153
chr11    3062997    3063296    Pos4    1    +    3062997    3063296    153,153,255
chr4    59868948    59869247    Neg5    1    -    59868948    59869247    153,255,153
chr6    92670855    92671154    Pos6    1    +    92670855    92671154    153,153,255
chr12    111937877    111938176    Pos7    1    +    111937877    111938176    153,153,255
chr13    26631633    26631932    Neg8    1    -    26631633    26631932    153,255,153
chr13    89216483    89216782    Neg9    1    -    89216483    89216782    153,255,153
chr7    122607914    122608213    Neg10    1    -    122607914    122608213    153,255,153

Do you think that I need to use a bed file runed after MACS or some other program?

Best,
Yuliang


PS: what is the sessionInfo()?

On Thu, Sep 16, 2010 at 5:45 PM, Zhu, Julie <Julie.Zhu@umassmed.edu> wrote:

uliang,

What is your test.bed look like? It should be a data frame.  If you have a bed file named test.bed, you would first read the test.bed into R as test.bed = read.table(“bedfile.txt”, sep=”\t”, skip=1,header=FALSE) before calling function BED2RangedData.

Could you please type test.bed[1:5,] to see what is the content of the first five rows of the data?

How many rows in test.bed data frame? Please include sessionInfo() in your email.

Please follow the examples by typing ?BED2RangedData in a R console.

Best regards,

Julie


On 9/16/10 6:50 PM, "Yuliang Tan" <yuliangtan@gmail.com <http://yuliangtan@gmail.com> > wrote:

Hi Julie,

Thanks for your help! I have another problem when i run BED2RangedData(test.bed,header=TRUE),
It got:
Error in DataFrame(...) : cannot coerce class "numeric" to a DataFrame
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(156,0xa02c9720) malloc: *** mmap(size=105365504) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Do you thin it is because of my bed or some packages i doesn't install?

Best,

Yuliang

On Thu, Sep 16, 2010 at 5:54 AM, Zhu, Julie <Julie.Zhu@umassmed.edu <http://Julie.Zhu@umassmed.edu> > wrote:
Hi Yuliang,

The mouse TSS annotation is TSS.mouse.NCBIM37. You can also get the annotation using the function getAnnotation.

You will find this information if you type in R console,
library(ChIPpeakAnno)
?annotatePeakInBatch
?getAnnotation

For detailed information on how to use the package, please refer to the paper in BMC Bioinformatics (http://www.biomedcentral.com/1471-2105/11/237) and ChIPpeakAnno practical presentation given at Bioc2010 conference (http://www.bioconductor.org/help/course-materials/2010/BioC2010/BioC2010_ChIPpeakAnno.pdf).

Kind regards,

Julie



On 9/15/10 9:42 PM, "Yuliang Tan" <yuliangtan@gmail.com <http://yuliangtan@gmail.com>  <http://yuliangtan@gmail.com> > wrote:

Hi Zhu:

I'm trying to do some analysis by ChIPpeakAnno, but it seems that there are no mouse genome database in this package, could you tell me how to build an annotation file for this package?  Thank you!





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