gzfile中的錯誤（fname，open =「rt」）：無效的「description」參數

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  

我的電腦有什麼問題？

> 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目前不處理「full_soft」文件的情況下，即GDS表達和與GDS相關聯的GPL信息的組合的文件。我已經在我的TODO列表上解析了full_soft格式。目前，避免「full_soft」文件格式也是我會推薦的。這樣做並不是問題，因爲在使用標準GEOquery工作流程導入GDS時，GEOquery將重新構建「full_soft」文件內容。