thomasKuilman
commented
8 years ago Hi Michael,
The cause for this message is (most likely) in the way you have started the analysis. CopywriteR consists of two important functions, CopywriteR.R and plotCNA.R. The thing is that what you would refer to as a control or reference has a different meaning for the two functions. While for the CopywriteR() function it refers to what sample should be used to determine where peak regions are (so that it knows which reads can be discarded as �on-target� reads), for the plotCNA function the control/reference refers to the data relative to which sample data are plotted. If you would run CopywriteR with the following sample.control
samples controls tumor.bam normal.bam
and run plotCNA, you get your error message. That is because the off-target analysis has not been performed on normal.bam. Instead you should have run CopywriteR with the following sample.control:
samples controls tumor.bam normal.bam normal.bam normal.bam
Now the off-target analysis is performed on normal.bam as well (using the peak region information that is retrieved from the sample itself), and you can use the data from normal.bam as a reference for relative plotting. Please also see https://github.com/PeeperLab/CopywriteR#all-bam-files-should-be-processed-by-copywriter on our GitHub page for a more elaborate explanation.
I hope that helps, please let me know if you still have trouble to run CopywriteR.
Best regards,
Thomas
Thomas Kuilman, PhD Department of Molecular Oncology Netherlands Cancer Institute 1066 CX Amsterdam The Netherlands
Phone: +31-20-5121841
On 20 Jul 2015, at 10:16, Michael P Schroeder notifications@github.com<mailto:notifications@github.com> wrote:
Hi
I've just used the copywriteR package to analyze a tumour-normal pair. After the execution I have run the plotCNA function as described. The output is that I should re-analyze the sample because it does not find the control.
plotCNA(file.path("PE08_copywriteR")) [1] "log2.PE08_ID-ready.bam" "log2.PE08_CR-ready.bam" [1] TRUE FALSE [1] "log2.PE08_CR-ready.bam" Error in plotCNA(file.path("PE08_copywriteR")) : The following samples refer to .bam files that have not been processed by CopywriteR: �log2.PE08_CR-ready.bam� . Please re-analyze all required samples using CopywriteR and run the plotCNA function again.
Something cannot be right, but I'm not able to guess what. Could you help me out on this?
Thanks Michael
� Reply to this email directly or view it on GitHubhttps://github.com/PeeperLab/CopywriteR/issues/6.
mpschr
Hi
I've just used the copywriteR package to analyze a tumour-normal pair. After the execution I have run the
plotCNAfunction as described. The output is that I should re-analyze the sample because it does not find the control.Something cannot be right, but I'm not able to guess what. Could you help me out on this?
Thanks Michael