Question

library(Biobase)    
library(GEOquery)    
gds4577 <- getGEO(filename='c:/test/GDS4577_full.soft.gz')    
eset <- GDS2eSet(gds4577, do.log2=TRUE)    
>  eset <- GDS2eSet(gds4577, do.log2=TRUE)    
File stored at:     
C:\DOCUME~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gzC:\DOCUME~1\sanya\LOCALS~1\Temp\RtmpQtuak0/GPL1261.annot.gz    
Error in gzfile(fname, open = "rt") : invalid 'description' argument    
In addition: Warning messages:    
1: In if (GSEMatrix & geotype == "GSE") { :    
  the condition has length > 1 and only the first element will be used    
2: In if (geotype == "GDS") { :    
  the condition has length > 1 and only the first element will be used    
3: In if (geotype == "GSE" & amount == "full") { :    
  the condition has length > 1 and only the first element will be used    
4: In if (geotype == "GSE" & amount != "full" & amount != "table") { :    
  the condition has length > 1 and only the first element will be used    
5: In if (geotype == "GPL") { :    
  the condition has length > 1 and only the first element will be used    
6: In if (!file.exists(destfile)) { :    
  the condition has length > 1 and only the first element will be used    
7: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :    
  only first element of 'url' argument used    
8: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :    
  only first element of 'destfile' argument used    
> eset    
Error: object 'eset' not found

我的电脑有什么问题？

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936  LC_CTYPE=Chinese_People's Republic of China.936   
[3] LC_MONETARY=Chinese_People's Republic of China.936 LC_NUMERIC=C                                      
[5] LC_TIME=Chinese_People's Republic of China.936    

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

other attached packages:
[1] GEOquery_2.28.0      BiocInstaller_1.12.0 affy_1.40.0          Biobase_2.22.0       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] affyio_1.30.0         preprocessCore_1.24.0 RCurl_1.95-4.1        tools_3.0.2           XML_3.98-1.1          zlibbioc_1.8.0

Answer 1

GEOquery目前不处理“full_soft”文件的情况，该文件是GDS表达式和与GDS相关联的GPL信息的组合。我已经在我的TODO列表中解析了full_soft格式。目前，我也建议避免使用“full_soft”文件格式。这样做不是问题，因为在使用标准GEOquery工作流导入GDS时，GEOquery将重建“full_soft”文件内容。

gzfile中的错误（fname，open =“rt”）：无效的'description'参数

1 个答案: