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Question: question regarding ChIPPeakAnno use
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gravatar for Julie Zhu
6.3 years ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:
Dear Xianyong, Thanks for the feedback! Regarding the error you got, it seems to be a memory issue. Could you please take a look at the post at http://www.mail- archive.com/r-help@stat.math.ethz.ch/msg91461.html? I am ccing the list to get input from the experts in memory setting and management. Best regards, Julie On 5/4/12 3:07 PM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu> wrote: Hi, Dear Dr.Zhu: I got nice results by using your software, and I am still using this soft ware to analyze other data, now I have the following problem and tried two days, I can't figured out, would you please help me to solve this problem, I am really appreciate! since the file is bigger than 60 Mb (after compressed), I can't send it directly. When I used the CHIPAnno software to analysis my data, as problem always exist as following: > test1.bed=read.table("/Users/xm5/Downloads/ChIPpeakAnno/data/CHIPJ3. bed", sep="\t", skip=0, header=FALSE) > CHIPJ3 = BED2RangedData(test1.bed, header=FALSE) > data(TSS.human.GRCh37) > annotatedPeak = annotatePeakInBatch(CHIPJ3, AnnotationData=TSS.human.GRCh37) Error: cannot allocate vector of size 14.4 Mb R(365,0xa0416540) malloc: *** mmap(size=15118336) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug I don't know what's reason, and I checked the file using other program, it looks OK, would you please help me to figure out, I appreciate your nice help please see the attached file that I used for this analysis. Best wishes, Xianyong [[alternative HTML version deleted]]
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