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> 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! [[alternative HTML version deleted]]

Hi Yuliang, 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> 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> 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=""> > 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! [[alternative HTML version deleted]]

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! [[alternative HTML version deleted]]

Hi Yuliang, When you do data(myPeakList), you are using the dataset myPeaklist from the package. In order to use your own dataset, you need to remove this line and assign a variable to the result of BED2RangedData. Here is the complete code. library(ChIPpeakAnno) test1.bed=read.table("~/Desktop/test1.bed", sep="\t", skip=1, header=FALSE) myPeakList = BED2RangedData(test1.bed,header=FALSE) data(TSS.mouse.NCBIM37) annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37) write.table(as.data.frame(annotatedPeak), file = "annotatedPeakList.xls", sep = "\t", row.names = FALSE) y = annotatedPeak$distancetoFeature[!is.na(annotatedPeak$distancetoFea ture) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS") #plot to show the distribution of my protein around TSS region (-5000, +1000) hist(y[y<=1000 | y>=-5000], xlab = "Distance To Nearest TSS") Best regards, Julie On 9/17/10 7:01 PM, "Yuliang Tan" <yuliangtan@gmail.com> wrote: Hi Julie: Unfortunately, it still doesn't work, it seems that i can't get a plot to show the distribution of my protein around TSS region (-5000, +1000) by ChIPpeakAnno. So i send you my bed file (attached) and the R code that i used in ChIPpeakAnno, could you tell why I failed to do this? ? library(ChIPpeakAnno) test1.bed=read.table("~/Desktop/test1.bed", sep="\t", skip=1, header=FALSE) BED2RangedData(test1.bed,header=FALSE) myPeakList=test1.bed data(myPeakList) annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37, output="both", multiple = F, maxgap = 0) write.table(as.data.frame(annotatedPeak), file = "annotatedPeakList.xls", sep = "\t", row.names = FALSE) y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS") Thanks! Best, Yuliang 2010/9/17 Zhu, Julie <julie.zhu@umassmed.edu> Yuliang, hist(y[abs(y<1000)], xlab = "Distance To Nearest TSS", main = "") should work. You can modify 1000 to whatever threshold you feel right. Best regards, Julie On 9/17/10 2:58 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> > wrote: Hi Julie: The code i used is : y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS", main = "", breaks = 1000, xlim = c(-5000, 1000)) It works very well when i tried the code that you sent it me$B!J(Bpls check it in the attached file. Thank you! Could you tell me how to figure a plot to show the region near to the TSS region? I think the result showed a too big range around TSS region. How to define y to just the Nearest fragments? y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromNearest == "NearestStart"] It doesn't work. Best, Yuliang On Fri, Sep 17, 2010 at 11:16 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> > wrote: Hi Yuliang, Your plot might have included all the overlapping fragments not just the nearest. What is the code you used for generating the plot? y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab="Distance To Nearest TSS") Best regards, Julie On 9/17/10 2:05 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> > wrote: Hi Julie: I still think that there must be some problems, the results are different with different software, and I think the results in my ChIPpeakAnno is strange, could you pls look at the results by chippeaklist and CEAS in the attached files?? Thanks! Best, Yuliang On Fri, Sep 17, 2010 at 10:50 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> > wrote: Hi Yuliang, The warning messages can be ignored for now. In the future release, I will replace the multiple argument with select argument. Best regards, Julie On 9/17/10 1:43 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> > wrote: Hi Julie: I'm sorry to bother you so many times, but there is another error message again, when I type >annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37, output="both", multiple = F, maxgap = 0) It showed: There were 19 warnings (use warnings() to see them) > warnings() Warning messages: 1: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 2: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 3: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 4: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 5: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 6: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 7: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 8: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 9: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 10: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 11: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 12: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 13: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 14: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 15: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 16: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 17: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 18: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 19: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. Do you know what's the problem? Thanks! Best, Yuliang On Fri, Sep 17, 2010 at 6:21 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> > wrote: 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 <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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 <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: 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($B!H(Bbedfile.txt$B!I(B, sep=$B!I(B\t$B!I(B, 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=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: 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=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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! [[alternative HTML version deleted]]

Hi Yuliang, I do not quite get what do you mean by selecting y. If you want to browse the gene list, you could select the gene list in the file you saved as annotatedPeakList.xls . write.table(as.data.frame(annotatedPeak), file = "annotatedPeakList.xls", sep = "\t", row.names = FALSE) Alternatively, you could look at the data as a data frame. Y = as.data.frame(annotatedPeak) Y[1:10,] I strong suggest you take a look at the introduction to R book at http://cran.r-project.org/doc/manuals/R-intro.pdf that will help you understand how R works. Best regards, Julie On 9/21/10 8:07 PM, "Yuliang Tan" <yuliangtan@gmail.com> wrote: Hi Julie, What could I do if I want to profile the expression of proteins in a special kind of genes promoters? I tried to select this genes from annotatedPeakList, but i don't know how to define y, so I can't plot it. best, Yuliang 2010/9/20 Zhu, Julie <julie.zhu@umassmed.edu> Yuliang, You are welcome! Best, Julie On 9/20/10 2:05 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> > wrote: Hi Julie, You really do me a great favor! Thank you so much! ? Best, Yuliang 2010/9/20 Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> > Hi Yuliang, When you do data(myPeakList), you are using the dataset myPeaklist from the package. In order to use your own dataset, you need to remove this line and assign a variable to the result of BED2RangedData. Here is the complete code. library(ChIPpeakAnno) ???????test1.bed=read.table("~/Desktop/test1.bed", sep="\t", skip=1, header=FALSE) myPeakList = BED2RangedData(test1.bed,header=FALSE) ??data(TSS.mouse.NCBIM37) annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37) write.table(as.data.frame(annotatedPeak), file = "annotatedPeakList.xls", sep = "\t", row.names = FALSE) y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS") #plot to show the distribution of my protein around TSS region (-5000, +1000) hist(y[y<=1000 | y>=-5000], xlab = "Distance To Nearest TSS") Best regards, Julie On 9/17/10 7:01 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> > wrote: Hi Julie: Unfortunately, it still doesn't work, it seems that i can't get a plot to show the distribution of my protein around TSS region (-5000, +1000) by ChIPpeakAnno. So i send you my bed file (attached) and the R code that i used in ChIPpeakAnno, could you tell why I failed to do this? ? library(ChIPpeakAnno) test1.bed=read.table("~/Desktop/test1.bed", sep="\t", skip=1, header=FALSE) BED2RangedData(test1.bed,header=FALSE) myPeakList=test1.bed data(myPeakList) annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37, output="both", multiple = F, maxgap = 0) write.table(as.data.frame(annotatedPeak), file = "annotatedPeakList.xls", sep = "\t", row.names = FALSE) y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> ?<http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS") Thanks! Best, Yuliang 2010/9/17 Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> > Yuliang, hist(y[abs(y<1000)], xlab = "Distance To Nearest TSS", main = "") should work. You can modify 1000 to whatever threshold you feel right. Best regards, Julie On 9/17/10 2:58 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> > wrote: Hi Julie: The code i used is : y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> ?<http: is.na=""> ?<http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab = "Distance To Nearest TSS", main = "", breaks = 1000, xlim = c(-5000, 1000)) It works very well when i tried the code that you sent it me$B!J(Bpls check it in the attached file. Thank you! Could you tell me how to figure a plot to show the region near to the TSS region? I think the result showed a too big range around TSS region. How to define y to just the Nearest fragments? y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> ?<http: is.na=""> ?<http: is.na=""/> (annotatedPeak$distancetoFeature) & annotatedPeak$fromNearest == "NearestStart"] It doesn't work. Best, Yuliang On Fri, Sep 17, 2010 at 11:16 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> > wrote: Hi Yuliang, Your plot might have included all the overlapping fragments not just the nearest. What is the code you used for generating the plot? y = annotatedPeak$distancetoFeature[!is.na <http: is.na=""> <http: is.na=""> ?<http: is.na=""> ?<http: is.na=""> (annotatedPeak$distancetoFeature) & annotatedPeak$fromOverlappingOrNearest == "NearestStart"] hist(y, xlab="Distance To Nearest TSS") Best regards, Julie On 9/17/10 2:05 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> > wrote: Hi Julie: I still think that there must be some problems, the results are different with different software, and I think the results in my ChIPpeakAnno is strange, could you pls look at the results by chippeaklist and CEAS in the attached files?? Thanks! Best, Yuliang On Fri, Sep 17, 2010 at 10:50 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> > wrote: Hi Yuliang, The warning messages can be ignored for now. In the future release, I will replace the multiple argument with select argument. Best regards, Julie On 9/17/10 1:43 PM, "Yuliang Tan" <yuliangtan@gmail.com <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> > wrote: Hi Julie: I'm sorry to bother you so many times, but there is another error message again, when I type >annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData = TSS.mouse.NCBIM37, output="both", multiple = F, maxgap = 0) It showed: There were 19 warnings (use warnings() to see them) > warnings() Warning messages: 1: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 2: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 3: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 4: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 5: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 6: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 7: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 8: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 9: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 10: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 11: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 12: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 13: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 14: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 15: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 16: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 17: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 18: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. 19: In .local(query, subject, maxgap, minoverlap, type, select,? ... : ? argument 'multiple' is deprecated; use 'select'. Do you know what's the problem? Thanks! Best, Yuliang On Fri, Sep 17, 2010 at 6:21 AM, Zhu, Julie <julie.zhu@umassmed.edu <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> > wrote: 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 <http:="" yuliangtan@gmail.com=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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 <http:="" julie.zhu@umassmed.edu=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: 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($B!H(Bbedfile.txt$B!I(B, sep=$B!I(B\t$B!I(B, 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=""> <http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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=""> <http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: julie.zhu@umassmed.edu=""> ?<http: 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=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: yuliangtan@gmail.com=""> ?<http: 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! [[alternative HTML version deleted]]