R语言,进行GEO数据挖掘与分析,在线下载GEO数据,
gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)
报以下错误:
Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Error: The size of the connection buffer (131072) was not large enough
to fit a complete line:
* Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`
Rstido默认链接缓存为131072字节,转换后131KB,0.131MB
但是你下载的数据大小>131072字节,所以我们需要调整默认连接缓存,以便正常下载
解决方法:
Sys.setenv("VROOM_CONNECTION_SIZE"=99999999)
代码实现:
> gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)
Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Error: The size of the connection buffer (111) was not large enough
to fit a complete line:
* Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`
> Sys.setenv("VROOM_CONNECTION_SIZE"=99999999)
> gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)
Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Rows: 18 Columns: 160
0s-- Column specification --------------------------------------------------------------------------------------------------------
Delimiter: "\t"
chr (1): ID_REF
dbl (159): GSM2493904, GSM2493905, GSM2493906, GSM2493907, GSM2493908, GSM2493909, GSM2493910, GSM2493911, GSM2493912, GSM24...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Using locally cached version of GPL23075 found here:
C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GPL23075.soft