Unable to run geo dataset from RnBeads, a lot questions - hope get an answer here

[colin...@gmail.com]

Hi, everyone, I am new to the field of genomics.

I am trying to run some geo data set via RnBeads on my windows 7 machine, I am getting this:

Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Bad access

I tried with just geoquery, same issue. 

But I can definitely access the ftp via windows or in a web page or any other ftp software.

I have 3 questions, hope someone can help me out:

1. does anyone know an issue to this problem, is this a bug in latest version of geoquery on windows platform?

2. is there a way I can download the geodataset manually to my hard drive disk, and run rnbeads, and tell it to load the geodataset from local disk? I can't find a way to do this via R documentation or vignette.

3. I can compare geodateset via the online GEO2R tool, is the output from GEO2R comparable to what I will get from RnBeads processing the geo dataset? if not, then I am fine with just sticking with the GEO2R gene list.

Any helps are greatly appreciated. Thanks a million in advance.

[Pavlo Lutsik]

Hi,

From your description it is clear that the problem is rooted outside of RnBeads. In case you manage to download the data set as a series matrix file you can use function "read.geo" to import it into RnBeads (it is rather well documented). Sorry, cannot give you any hints about GEO2R.

Best regards,

Pavlo