Question: Help for TCGA CNV data error.
0
gravatar for BioLite
15 months ago by
BioLite20
BioLite20 wrote:

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!!

cnv tcga • 449 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe54k • written 15 months ago by BioLite20
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

Hello,

You just have to do this:

load("lihcnocnvhg19.rda")

Kevin

ADD COMMENTlink written 15 months ago by Kevin Blighe54k

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...

ADD REPLYlink written 15 months ago by BioLite20

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

load("lihcnocnvhg19.rda")
ADD REPLYlink modified 15 months ago • written 15 months ago by Kevin Blighe54k
1

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

ADD REPLYlink written 15 months ago by BioLite20

You are welcome, BioLite!

ADD REPLYlink written 15 months ago by Kevin Blighe54k
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