Hello ,

 I want to collect a raw data or an expression dataset for breast cancer as a validation for my project. But I did not find within my purpose:

1) tumor-normal samples 

2) affy

Is there anyone who used to have this dataset or information please?

Could you give me a GEO link or website?

Regards,

Tahani,

hi Tahani,

you should check the GEOmetadb BioC package that will allow you to interrogate the Gene Expression Omnibus database for the data you are looking for. The vignette of the package is a good starting point, it has several examples that you can adapt to your needs.

cheers,

robert.

Thanks , but I faced some problem while I downloading some thing in R like :

if(!file.exists('GEOmetadb.sqlite')) getSQLiteFile()

 trying URL 'http://dl.dropbox.com/u/51653511/GEOmetadb.sqlite.gz'
Content type 'application/octet-stream' length 272661479 bytes (260.0 MB)
downloaded 66.5 MB

Unzipping...
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: database disk image is malformed
In addition: Warning messages:
1: In url(url_geo_1, open = "rb") :
  InternetOpenUrl failed: '‏‏انتهت مهلة العملية'
2: In url(url_geo_2, open = "rb") :
  cannot open: HTTP status was '403 Forbidden'
3: In download.file(url_geo, destfile = localfile, mode = "wb") :
  downloaded length 69693440 != reported length 272661479
4: closing unused connection 3 (http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz)
5: In file.remove(filename) :
  cannot remove file 'C:/Users/SONY/Documents/myproject/CELCEL/CELfiles/GEOmetadb.sqlite.gz', reason 'Permission denied'
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: database disk image is malformed

Hi,

from your output it looks like the database (.sqlite.gz) file has not been properly downloaded. This file should take actually a few Gbytes so the message that 66.5 MB have been downloaded indicates that something went wrong when doing this first step.

Please make sure that you are running the latest R 3.2.2 and the latest version of GEOmetadb. Please show the output of the command sessionInfo() if you are unsure about this.

Maybe you should check with your local system administrator about these connectivity issues.

cheers,

robert.