error message

Question

TCGAbiolinks DNA methylation analysis TCGAvisualize_meanMethylation

0

Entering edit mode

maedakus ▴ 10

@maedakus-9484

Last seen 7.6 years ago

Hi,

i am very new to bioconductor, and now i am planning to analyis the DNA methylation analysis using TCGAbiolinks.

i preferred the links below and copy & pasted it , but the R script does not work well and the error comes out.

if you know the solution, would you tell me , thanks in advance !

TCGAvisualize_meanMethylation(coad.met,
                              groupCol = "methylation_subtype",
                              subgroupCol = "hypermutated",
                              shapes=NULL,
                              print.pvalue=TRUE,
                              ylab="DNA methylation",
                              xlab=NULL,
                              title="Mean DNA methylation",
                              labels=NULL,
                              group.legend  = "Groups",
                              subgroup.legend = "hypermutated",
                              filename = "coad_mean.png")

error message;

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains invalid names

https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#case-study-n.-3-integration-of-methylation-and-expression-for-coad

tcgabiolinks • 3.0k views

ADD COMMENT • link updated 8.1 years ago by Tiago C. Silva ▴ 270 • written 8.1 years ago by maedakus ▴ 10

0

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Hi, could you give the version of the package?

I made a change in the code recently and probably there is no subtype information in the object.

I will update the vignette.

I believe the solution will be preparing with the add.subtypes parameter as true.

coad.exp <- TCGAprepare(query = coad.query.exp,
                        add.subtype = TRUE,
                        dir = "/dados/ibm/comparing/biolinks/RNA/",
                        type = "rsem.genes.results",
                        save = T,filename = "coadexp.rda")

ADD REPLY • link 8.1 years ago Tiago C. Silva ▴ 270

0

Entering edit mode

Hi, thank you so much for help.

version of TCGAbiolinks is as below

> packageVersion("TCGAbiolinks")
[1] ‘1.0.9’

ADD REPLY • link 8.1 years ago maedakus ▴ 10

score 0 · Answer 1 · 2016-03-29

Hi,

when conducting the TCGAbiolinks, i have succeeded in the process of TCGAdownload and TCGAprepare as below. i downloaded data for sure.

but as a next step, TCGAvisualize_meanMethylation does not work well. i put the sentence " add.subtype = TRUE" in the

script as you suggested , but it does not work and comes out error, as below.

query.met <- TCGAquery(tumor = c("PAAD"),platform = "HumanMethylation450",level = 3)
TCGAdownload(query.met, path = "C:/Users/146790/NCBI GEO/TCGA database")

coad.met <- TCGAprepare(query = query.met,
                        dir = "C:/Users/146790/NCBI GEO/TCGA database",
                        save = TRUE,
                       
                        filename = "metcoad.rda",
                        reannotate = TRUE)

error message

> TCGAvisualize_meanMethylation(coad.met,
+                               groupCol = "methylation_subtype",
+                               subgroupCol = "hypermutated",
+                               shapes="NULL",
+                               print.pvalue=TRUE,
+                               ylab="DNA methylation",
+                               xlab="NULL",
+                               add.subtype = TRUE,
+                               title="Mean DNA methylation",
+                               labels="NULL",
+                               group.legend  = "Groups",
+                               subgroup.legend = "hypermutated",
+                               filename = "coad_mean.png")
Error in TCGAvisualize_meanMethylation(coad.met, groupCol = "methylation_subtype",  :
  unused argument (add.subtype = TRUE)

score 0 · Answer 2 · 2016-03-29

0

Entering edit mode

Tiago C. Silva ▴ 270

@tiagochst-7121

Last seen 10 months ago

Miami, US

The devel manual is correct. The add.subtype is used in TCGAprepare function only.
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#case-study-n.-3-integration-of-methylation-and-expression-for-coad

Also, for the PAAD we don't have any subtype information for the moment. So when you prepare the data you don't have the informations you requested (hypermutated,methylation_subtype). An example of the code would be as below:

ADD COMMENT • link 8.1 years ago Tiago C. Silva ▴ 270

0

Entering edit mode

Hi,

thank you so much for cordial help.

i followed the script which you suggested , and run it , but the error has come out again.

coad.met <- TCGAprepare(query = query.met,
                        dir = "/dados/ibm/comparing/biolinks/coad/",
                        save = TRUE,
                        add.subtype = TRUE,
                        filename = "metcoad.rda",
                        reannotate = TRUE)

error message

> coad.met <- TCGAprepare(query = query.met,
+                         dir ="C:/Users/146790/NCBI GEO/TCGA database",
+                         save = TRUE,
+                         add.subtype = TRUE,
+                         filename = "metcoad.rda",
+                         reannotate = TRUE)
Error in TCGAprepare(query = query.met, dir = "C:/Users/146790/NCBI GEO/TCGA database", :
unused argument (add.subtype = TRUE)

<font style="background-color: rgb(255, 255, 0);">version of TCGAbiolinks is as below</font>

> packageVersion("TCGAbiolinks")
[1] ‘1.0.9’

ADD REPLY • link 8.1 years ago maedakus ▴ 10

0

Entering edit mode

Hi,

Actually the code is there, but I didn't update the version number. 1.0.10 should be ok, but it will only be in bioconductor tomorrow.

But if you try to reinstall it, it should work.

source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

I'm sorry for the inconvenience.

ADD REPLY • link 8.1 years ago Tiago C. Silva ▴ 270