[BioC] Loading eSet.r objects from ArrayExpress

[Maciej Jończyk]

Hi,

I have similar problem:

> source("E-GEOD-31763.eSet.r")
Błąd w *error in* source("E-GEOD-31763.eSet.r") :
   niepoprawny wielobajtowy znak w parserze w linii 11 *invalid 
multibyte character in parser in line 11*
Dodatkowo: Było 50 lub więcej ostrzeżeń (użyj 'warnings()' aby zobaczyć 
pierwsze 50) *additionaly, there were 50 or more warnings*
> warnings()
Komunikaty ostrzegawcze: *warnings*
1: In grepl("\n", lines, fixed = TRUE) :
   niepoprawny łańcuch wejściowy 11 w lokalizacji *invalid input string 
11 in localization*


> source("E-GEOD-23917.eSet.r")
Błąd w *error in* source("E-GEOD-23917.eSet.r") :
   E-GEOD-23917.eSet.r:29:1: nieoczekiwano: ',' *not expected*
28:
29: ,
     ^
Dodatkowo: Było 50 lub więcej ostrzeżeń (użyj 'warnings()' aby zobaczyć 
pierwsze 50) *additionaly, there were 50 or more warnings*


I suspect there are errors in the files.

Here is my sessioninfo
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=pl_PL.UTF-8       LC_NUMERIC=C               
LC_TIME=pl_PL.UTF-8
  [4] LC_COLLATE=pl_PL.UTF-8     LC_MONETARY=pl_PL.UTF-8    
LC_MESSAGES=pl_PL.UTF-8
  [7] LC_PAPER=pl_PL.UTF-8       LC_NAME=C                  LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=pl_PL.UTF-8 
LC_IDENTIFICATION=C

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

other attached packages:
[1] ArrayExpress_1.20.0 affy_1.38.1         Biobase_2.20.1      
Biostrings_2.28.0
[5] IRanges_1.18.4      BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] affyio_1.28.0         BiocInstaller_1.10.4  limma_3.16.8          
preprocessCore_1.22.0
[5] stats4_3.0.2          tools_3.0.2           XML_3.98-1.1          
zlibbioc_1.6.0

Best Wishes,
Maciej
-- 
Dr Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



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