Question: Downloading .CEL files from GEO
2
gravatar for alara
4.0 years ago by
alara20
alara20 wrote:

Hi,

I would like to download all .CEL files from samples with specific characteristics.  

For example, I need to obtain all .CEL files with “normal skin” (or any other characteristic “fibroblasts”, “nephroblastoma”, “breast cancer tumor”, etc. ) from all GEO Datasets/Series on GPL570 platform.

Now I search datasets. read "Sample information" on GEO and download it manually.

I found database http://metadb.bmes.nthu.edu.tw/m2db/Index.html . But it is not enough.

How can I do this automatically? Does such soft or script exist? Or any idea how can I do this script in R (books, article, etc)?

R geo • 3.5k views
ADD COMMENTlink modified 4.0 years ago by Sean Davis25k • written 4.0 years ago by alara20
4
gravatar for Sean Davis
4.0 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The GEOmetadb Bioconductor package will allow you to query for all GSMs with CEL files for GPL570.  From there, you can use GEOquery getGEOSuppFiles().  

Alternatively, you can just get all GSMs from the GPL570 record; there is an example of doing something similar in the GEOquery vignette.  There may be some GSMs that do not have CEL files, but getGEOSuppFiles() will simply not return results for those GSMs.

 

  

ADD COMMENTlink written 4.0 years ago by Sean Davis25k
2
gravatar for Devon Ryan
4.0 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

I suspect that Sean Davis has a better method, but what I've always done is:

  1. Get a list of the datasets that I want from the GEO web interface
  2. Use the GEOquery R package to then download and use the CEL files (if they exist, you can also get the "soft" files if not) in R.

The GEOquery package is pretty handy for fetching datasets, but I don't think it also lets you search for them with keywords (though that would be really nice!).

Edit: As I had suspected, see Sean's answer.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Devon Ryan88k

How to download multiple GSE related CEL files EX: GSE 50697, GSE 43837 and more such id at once using GEOQuery. Script will be appreciated. I would be very thankful if anyone can help me in this matter. Its little urgent, so kindly provide me your reply soon.

Thanks in advance!!

ADD REPLYlink written 14 months ago by sndbt12310
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