Help for TCGA CNV data error.

Question

[BioLite]

Hi, I'm analyzing TCGA CNV data, following the workflow in TCGAWorkflow(https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#genomic_analysis), I write code as following to get TCGA-LIHC' CNV data:

#Genomic analysis
query.lihc.nocnv <-GDCquery(project = "TCGA-LIHC",
                            data.category = "Copy number variation",
                            legacy = TRUE,
                            file.type = "nocnv_hg19.seg",
                            sample.type = c("Primary solid Tumor"))
GDCdownload(query.lihc.nocnv)
lihc.nocnv <- GDCprepare(query.lihc.nocnv, save = TRUE, save.filename = "lihcnocnvhg19.rda")

And then, R informs me like this:

Reading copy number variation files
  |===============================================================| 100%
Saving file:lihcnocnvhg19.rda

It seems s that my codes work well. However, when I read data which have been saved in the above code,data(lihcnocnvhg19), I get a Warning message: In data(lihcnocnvhg19) : Without‘lihcnocnvhg19’dataset.

Sorry for my poor analysis experience, maybe there are some helpful person can point my faulty? Thanks very much!!

Answer 1

[Kevin Blighe]

Hello,

You just have to do this:

load("lihcnocnvhg19.rda")

Kevin

[BioLite]

Dear Kevin, Thanks for your help, but the error still exists.

load(lihcnocnvhg19.rda)
Error in load(lihcnocnvhg19.rda) : object 'lihcnocnvhg19.rda' not found

Maybe there are some faults in my GDCquery() arguments? Crying...

[Kevin Blighe]

Hey, where are the quotation marks in your code? Try this:

load("lihcnocnvhg19.rda")

[BioLite]

Woo... It works well. Embarrassing and sorry for my careless.. Thank you, handsome and kind Kevin.

[Kevin Blighe]

You are welcome, BioLite!