Question: Downloading multiple samples with GEO accesion numbers
0
gravatar for osieman52
2.9 years ago by
osieman5220
osieman5220 wrote:

Dear all,

I have GEO accession numbers for 850 samples I would like to download. What is the easiest way to download a bulk of data from GEO database. I know that it can be done with a ftp or by using R (geoQuery). But I'am not sure how. Can someone please help me or give me advice on how to do this. I am new to this. Here is a link to the paper where the accession numbers can be found in the supplementary : https://academic.oup.com/biostatistics/article/11/2/242/268035?searchresult=1

Example of the accession numbers : GSM20894 GSM20961 GSM20943 GSM20836 GSM20817

Thanks in advance!

microarray geo • 1.8k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by osieman5220
1
gravatar for osieman52
2.9 years ago by
osieman5220
osieman5220 wrote:

Solution in R:

library(GEOquery)

x <- as.list(scan("files_with_GEO_accesionCodes.txt", what ="" , sep = "" ))

files = lapply(x, getGEOSuppFiles)

ADD COMMENTlink written 2.9 years ago by osieman5220

how do you write the input in file?

ADD REPLYlink written 5 months ago by smrutimayipanda10
1
gravatar for Sej Modha
2.9 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

A: How to download raw data in batch from NCBI based on Series Accession number or

ADD COMMENTlink written 2.9 years ago by Sej Modha4.7k

Thanks for the link but, unfortunately this doesn't provide enough information to help me out.

ADD REPLYlink written 2.9 years ago by osieman5220

Have you tried the solution provided on the post linked above? What is the preferred format of download for the data?

ADD REPLYlink written 2.9 years ago by Sej Modha4.7k

osieman52 : That solution is using NCBI unix utilities. You can find more information on those here.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by GenoMax94k

and on the GEO help page.

ADD REPLYlink written 2.9 years ago by Sej Modha4.7k

I managed to find an easy way to download the files I need by using R.

library(GEOquery) x <- as.list(scan("files_with_GEO_accesionCodes", what ="" , sep = "" )) files = lapply(x, getGEOSuppFiles)

Thank you for the responds!

ADD REPLYlink written 2.9 years ago by osieman5220

A small question added to this quetions, how would one find the batch IDs of the downloaded files? I want to create vectors in orderer to do this I need batch ids. How could I find or generate these batch ids ?

ADD REPLYlink written 2.9 years ago by osieman5220

Were you able to find the solution to making a vector with all the GSM(GEO sample accession numbers)?

ADD REPLYlink written 13 months ago by sparshnegi70
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