doubts regarding opening rda file

hii, I have created rda file by using this code.

query.exp.hg38 <- GDCquery(project = "TCGA-GBM", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ", barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"))
GDCdownload(query.exp.hg38)
expdat <- GDCprepare(query = query.exp.hg38, save = TRUE, save.filename = "exp.rda")

while trying to open that rda file,i am getting primitive error.load("exp.rda") show(exp) function (x) .Primitive("exp") how to save a file like this?? save(dataBRCA, geneInfo , file = "dataGeneExpression.rda") If anybody knows please post the answer.

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written 9.5 years ago by ravipriya11396 •

I tried some code formatting on your post, to increase readability. I would like to encourage you to do the same, using the 101010 button. I think I got the first part right, but after error.load... I'm not so sure about the line breaks.

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written 9.5 years ago by WouterDeCoster

What do you mean by 101010 button?

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written 9.5 years ago by ravipriya11396 •

When you respond (please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized) there is a set of buttons that show up at the top of the edit window. It is the fifth button from the left. Select part of the text that represents code and then click that button to format it like you see if your original post.

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written 9.5 years ago by GenoMax

    dataNorm <- TCGAanalyze_Normalization(tabDF = BRCA, geneInfo =  geneInfo)
Error in as.vector(x) : no method for coercing this S4 class to a vector
In addition: Warning messages:
1: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript is an array, passing it thru as.vector() first
2: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript is an array, passing it thru as.vector() first
3: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript is an array, passing it thru as.vector() first
4: In NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript is an array, passing it thru as.vector() first

I am getting this error.But i don't know how to overcome this problem.please give any suggestion.

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updated 9.5 years ago by GenoMax

• written 9.5 years ago by ravipriya11396 •

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