Question: TCGAbiolinks DNA methylation analysis TCGAvisualize_meanMethylation
0
3.8 years ago by
maedakus10
maedakus10 wrote:

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",


error message;

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

modified 3.8 years ago by tiagochst150 • written 3.8 years ago by maedakus10

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,
type = "rsem.genes.results",
save = T,filename = "coadexp.rda")

Hi, thank you so much for help.

version of TCGAbiolinks is as below

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

0
3.8 years ago by
maedakus10
maedakus10 wrote:

Hi,

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)

dir = "C:/Users/146790/NCBI GEO/TCGA database",
save = TRUE,

reannotate = TRUE)

# error message

> 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",
Error in TCGAvisualize_meanMethylation(coad.met, groupCol = "methylation_subtype",  :
unused argument (add.subtype = TRUE)

0
3.8 years ago by
tiagochst150
Brazil
tiagochst150 wrote:

The devel manual is correct. The add.subtype is used in TCGAprepare function only.

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:

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,
save = TRUE,
reannotate = TRUE)

error message

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

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

[1] ‘1.0.9’

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.