Hi Gary- The plot should appear in the lower-left pane, which has tabs for Files, Plots, Packages, etc. I see in the screenshot that the pane is there and set to Plots, but it may be too small to show the plot -- you can try making the console pane smaller to enlarge the plot pane. I also see that you are using a somewhat dated version of R and hence of the DiffBind (and all other Bioconductor) packages. If possible, you may want to try updating to the most recent released version of R (v. 3.1.0) and reloading Bioconductor 2.14. Cheers- Rory On 04/06/2014 19:39, "???" <d92b41001 at="" ntu.edu.tw=""> wrote: >Hi Gordon, > >Thank you so much. Based on your suggestion, I can successfully input my >data as in the attached fig1. However, after typing >dba.plotHeatmap(feather), there is only a matrix, but no heat map graph >(fig2). I am sorry, this is the first time I perform R, could you teach >me >how to get a heat map figure? Many thanks. > >Gary > >-----????----- >From: Gordon Brown >Sent: Wednesday, June 04, 2014 1:13 AM >To: ??? >Cc: Rory Stark >Subject: Re: Could yo help us about DiffBind error > >Hi, Gary, > >Try telling DiffBind what the peak format is, like so: > >> feather = dba (sampleSheet="feather.csv",peakFormat="bed") > >The default format (if I recall correctly) is "raw", not "bed". > >Hope this helps, > >- Gord > >--------------------------------------------------------------------- - > > >From: ??? <d92b41001 at="" ntu.edu.tw=""> >Date: Tuesday, 3 June 2014 19:25 >To: Rory Stark <rory.stark at="" cruk.cam.ac.uk="">, Gord Brown ><gordon.brown at="" cruk.cam.ac.uk=""> >Subject: Could yo help us about DiffBind error > > >>Dear Rory and Gordon, >> >>I would like to use the DiffBind to analyze our ChIP-Seq data. I can run >>tamoxifen example in RStudio (fig1, the >> right side). However, when I run our own data, there are some errors as >>the below and the left side of fig1. The attached are two .bed files of >>our samples peak called by MACS (the fifth column is the enrichment fold >>change) and our sample sheet. Could you >> help us to solve this problem? Many thanks. >> >>> feather = dba (sampleSheet="feather.csv") >>FE7_K27ac_PW25 Feather H3K27ac E7 >>1 raw >>FE7_K27ac_PW51 Feather H3K27ac E7 >>2 raw >>? >>Error in if (res >= minval) { : missing value where TRUE/FALSE needed >>> warnings() >>Warning messages: >>1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>? >> >>Gary

Hi Rory, Thanks you so much. I will try what you suggest. Gary -----????----- From: Rory Stark Sent: Thursday, June 05, 2014 3:49 AM To: ??? Cc: Gordon Brown ; bioconductor at r-project.org Subject: Re: Could you help us about DiffBind Hi Gary- The plot should appear in the lower-left pane, which has tabs for Files, Plots, Packages, etc. I see in the screenshot that the pane is there and set to Plots, but it may be too small to show the plot -- you can try making the console pane smaller to enlarge the plot pane. I also see that you are using a somewhat dated version of R and hence of the DiffBind (and all other Bioconductor) packages. If possible, you may want to try updating to the most recent released version of R (v. 3.1.0) and reloading Bioconductor 2.14. Cheers- Rory On 04/06/2014 19:39, "???" <d92b41001 at="" ntu.edu.tw=""> wrote: >Hi Gordon, > >Thank you so much. Based on your suggestion, I can successfully input my >data as in the attached fig1. However, after typing >dba.plotHeatmap(feather), there is only a matrix, but no heat map graph >(fig2). I am sorry, this is the first time I perform R, could you teach >me >how to get a heat map figure? Many thanks. > >Gary > >-----????----- >From: Gordon Brown >Sent: Wednesday, June 04, 2014 1:13 AM >To: ??? >Cc: Rory Stark >Subject: Re: Could yo help us about DiffBind error > >Hi, Gary, > >Try telling DiffBind what the peak format is, like so: > >> feather = dba (sampleSheet="feather.csv",peakFormat="bed") > >The default format (if I recall correctly) is "raw", not "bed". > >Hope this helps, > >- Gord > >--------------------------------------------------------------------- - > > >From: ??? <d92b41001 at="" ntu.edu.tw=""> >Date: Tuesday, 3 June 2014 19:25 >To: Rory Stark <rory.stark at="" cruk.cam.ac.uk="">, Gord Brown ><gordon.brown at="" cruk.cam.ac.uk=""> >Subject: Could yo help us about DiffBind error > > >>Dear Rory and Gordon, >> >>I would like to use the DiffBind to analyze our ChIP-Seq data. I can run >>tamoxifen example in RStudio (fig1, the >> right side). However, when I run our own data, there are some errors as >>the below and the left side of fig1. The attached are two .bed files of >>our samples peak called by MACS (the fifth column is the enrichment fold >>change) and our sample sheet. Could you >> help us to solve this problem? Many thanks. >> >>> feather = dba (sampleSheet="feather.csv") >>FE7_K27ac_PW25 Feather H3K27ac E7 >>1 raw >>FE7_K27ac_PW51 Feather H3K27ac E7 >>2 raw >>? >>Error in if (res >= minval) { : missing value where TRUE/FALSE needed >>> warnings() >>Warning messages: >>1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>? >> >>Gary

Hi Rory, Thank you very much. The problem could be my version of R is too old. After updating to R v. 3.1.0, I can successfully produce results as the attached pictures. Your tool is really cool. Thanks again. Gary -----????----- From: Rory Stark Sent: Thursday, June 05, 2014 3:49 AM To: ??? Cc: Gordon Brown ; bioconductor at r-project.org Subject: Re: Could you help us about DiffBind Hi Gary- The plot should appear in the lower-left pane, which has tabs for Files, Plots, Packages, etc. I see in the screenshot that the pane is there and set to Plots, but it may be too small to show the plot -- you can try making the console pane smaller to enlarge the plot pane. I also see that you are using a somewhat dated version of R and hence of the DiffBind (and all other Bioconductor) packages. If possible, you may want to try updating to the most recent released version of R (v. 3.1.0) and reloading Bioconductor 2.14. Cheers- Rory On 04/06/2014 19:39, "???" <d92b41001 at="" ntu.edu.tw=""> wrote: >Hi Gordon, > >Thank you so much. Based on your suggestion, I can successfully input my >data as in the attached fig1. However, after typing >dba.plotHeatmap(feather), there is only a matrix, but no heat map graph >(fig2). I am sorry, this is the first time I perform R, could you teach >me >how to get a heat map figure? Many thanks. > >Gary > >-----????----- >From: Gordon Brown >Sent: Wednesday, June 04, 2014 1:13 AM >To: ??? >Cc: Rory Stark >Subject: Re: Could yo help us about DiffBind error > >Hi, Gary, > >Try telling DiffBind what the peak format is, like so: > >> feather = dba (sampleSheet="feather.csv",peakFormat="bed") > >The default format (if I recall correctly) is "raw", not "bed". > >Hope this helps, > >- Gord > >--------------------------------------------------------------------- - > > >From: ??? <d92b41001 at="" ntu.edu.tw=""> >Date: Tuesday, 3 June 2014 19:25 >To: Rory Stark <rory.stark at="" cruk.cam.ac.uk="">, Gord Brown ><gordon.brown at="" cruk.cam.ac.uk=""> >Subject: Could yo help us about DiffBind error > > >>Dear Rory and Gordon, >> >>I would like to use the DiffBind to analyze our ChIP-Seq data. I can run >>tamoxifen example in RStudio (fig1, the >> right side). However, when I run our own data, there are some errors as >>the below and the left side of fig1. The attached are two .bed files of >>our samples peak called by MACS (the fifth column is the enrichment fold >>change) and our sample sheet. Could you >> help us to solve this problem? Many thanks. >> >>> feather = dba (sampleSheet="feather.csv") >>FE7_K27ac_PW25 Feather H3K27ac E7 >>1 raw >>FE7_K27ac_PW51 Feather H3K27ac E7 >>2 raw >>? >>Error in if (res >= minval) { : missing value where TRUE/FALSE needed >>> warnings() >>Warning messages: >>1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>? >> >>Gary