Problem regarding get a column metadata

[git-jrwang]

Hi:

I try your example code to get column metadata from the sample .gctx file. It gives me an error as follow:
Error in withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) :
invalid multibyte string at '<84>'
I am not sure what happens?

[tnat1031]

Hi @git-jrwang , sorry you are having a problem. Can you please post the command you are running? Also does this work for you (from within R console)?

library(cmapR)
example("read.gctx.meta")

[git-jrwang]

I can read row meta, but not column meta. Here is the output of code.

library("cmapR")
Loading required package: rhdf5
Loading required package: data.table
data.table 1.10.4
The fastest way to learn (by data.table authors): https://www.datacamp.com/courses/data-analysis-the-data-table-way
Documentation: ?data.table, example(data.table) and browseVignettes("data.table")
Release notes, videos and slides: http://r-datatable.com
example("read.gctx.meta")

rd.gc.> gct_file <- system.file("extdata", "modzs_n272x978.gctx", package="cmapR")

rd.gc.> # row meta
rd.gc.> row_meta <- read.gctx.meta(gct_file)

rd.gc.> str(row_meta)
'data.frame': 978 obs. of 6 variables:
$ id : chr "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
$ is_bing : int 1 1 1 1 1 1 1 1 1 1 ...
$ is_lm : int 1 1 1 1 1 1 1 1 1 1 ...
$ pr_gene_id : int 5720 466 6009 2309 387 3553 427 5898 23365 6657 ...
$ pr_gene_symbol: chr "PSME1" "ATF1" "RHEB" "FOXO3" ...
$ pr_gene_title : chr "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)" "activating transcription factor 1" "Ras homolog enriched in brain" "forkhead box O3" ...

rd.gc.> # column meta
rd.gc.> col_meta <- read.gctx.meta(gct_file, dimension="column")
Error in withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning")) :
invalid multibyte string at '<84>'

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Traditional)_Taiwan.950
[2] LC_CTYPE=Chinese (Traditional)_Taiwan.950
[3] LC_MONETARY=Chinese (Traditional)_Taiwan.950
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Traditional)_Taiwan.950

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

other attached packages:
[1] cmapR_1.0 data.table_1.10.4 rhdf5_2.20.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.22.0 compiler_3.4.1 tools_3.4.1

[git-jrwang]

I have found problem myself. It is my LC_Locale. If I change to English, the problem solved.

[tnat1031]

@git-jrwang great, thanks for letting us know about that and glad you could solve the problem.