Input data from FinalReport generated by illumina

[Anonymous]

Hi, Charles,

I am trying to use your pipeline to analysis my DNA methylation data and further to integrate GEP data with it. I tested with your demo data which went through the procedures with minify and then COHCAP. Since you said the FinalReport generated by GenomeStudio can be read as well, and the advantage of this is that we can use GenomeStudio to normalize data, therefore I would like to try this way. I followed the instructions listed in the "COHCAP_Input_Files" to generate the FinalReport from GenomeStudio and prepared the samplist.txt. I found that I have to remove the description part located on the top of the FinalReport to be read and go through the code "beta.table <- COHCAP.annotate(beta.file, project.name, project.folder, platform="450k-UCSC")", but when check the beta.table, there is nothing inside. Below are the codes and results. Please help me solve the problem.

Thank you very much!

Sincerely,

Xin Li, Ph.D.
Assistant Professor
Myeloma Institute
University of Arkansas for Medical Sciences
Tel: 501 526 6990 x 8939
Email: lixin@uams.edulixin@uams.edu

code chunk number 1: inputVariables

library("COHCAP")

dir <- "C:/Users/lixin/Lab Jobs/Ongoing projects/MSC Studies/DNA Methylation Analysis/COHCAP analysis/GenomeStudioReports/Test for Methy&GEP for the first chips"
beta.file <- file.path(dir,"FinalReport.txt")

sample.file <- file.path(dir,"SampleSheet_Methyl_12_2014.txt")
project.folder <- "C:/Users/lixin/Lab Jobs/Ongoing projects/MSC Studies/DNA Methylation Analysis/COHCAP analysis/GenomeStudioReports/Test for Methy&GEP for the first chips/COHCAP results"
project.name <- "Methylation Analysis_052115"

code chunk number 2: annotation

beta.table <- COHCAP.annotate(beta.file, project.name, project.folder,
+ platform="450k-UCSC")
[1] 485577 12
[1] 0 16

list(sample.file)
[[1]]
[1] "C:/Users/lixin/Lab Jobs/Ongoing projects/MSC Studies/DNA Methylation Analysis/COHCAP analysis/GenomeStudioReports/Test for Methy&GEP for the first chips/SampleSheet_Methyl_12_2014.txt"

list(beta.table)
[[1]]
[1] SiteID Chr Loc Gene Island X10006044031_R03C02.AVG_Beta X10006044031_R04C02.AVG_Beta
[8] X10006044031_R05C02.AVG_Beta X10006044031_R06C02.AVG_Beta X10006044031_R01C01.AVG_Beta X10006044031_R01C02.AVG_Beta X10006044031_R02C01.AVG_Beta X10006044031_R02C02.AVG_Beta X10006044031_R03C01.AVG_Beta
[15] X10006044031_R05C01.AVG_Beta X10006044031_R06C01.AVG_Beta
<0 rows> (or 0-length row.names)

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[Charles Warden]

Hi Xin,

It is hard for me to tell what is the problem: can you try saving all the files in paths that don't have any spaces? For example, "C:/Users/lixin/Lab Jobs" could be converted to "C:/Users/lixin/Lab_Jobs" (but it would probably just be easier to save in a different location, like a new folder called "C:/COHCAP").

If that doesn't work, can you attach or copy in the first 10 lines of the report file from Genome Studio? I can then try troubleshooting the code from my end.

Thanks,
Charles

[Anonymous]

Hi Xin, hi Charles,

I think I have a very similar problem here. It seems like the annotation does not work (see "<0 rows> (or 0-length row.names)" posted by Xin. I get the same message when running COHCAP.annotate; when I try to run COHCAP.site, it stops with
[1] "Reading Sample Description File...."
Fehler in 6:ncol(beta.table) : Argument der Länge 0
(sorry about the german).
My guess is that he should read in Column 6 from the annotated file, but as that went wrong, he can't find anything.
Dear Charles, would you have any suggestion or clue what could have went wrong?
Best
Chris