Tutorial: GEO datasets: Raw data is available on Series record
0
gravatar for aharnishi02
2.6 years ago by
aharnishi0270
India
aharnishi0270 wrote:

I am new to lot of these genomics efforts. I have some basic questions on expression datasets found in GEO. The raw files of some datasets are indicated to be available on series record. (eg: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42133)

I could not find the raw files anywhere within the series record. Where do you suppose I could find these raw data?

expression array tutorial ncbi • 2.4k views
ADD COMMENTlink modified 2.6 years ago by mastal5112.0k • written 2.6 years ago by aharnishi0270

Does not look like the raw data is available for this accession.

ADD REPLYlink written 2.6 years ago by genomax57k

I had mailed the authors asking for the raw files, they reiterated that the raw files have been submitted and available online for download.

So what do you think i can do to get access to these files?

ADD REPLYlink written 2.6 years ago by aharnishi0270

@mastal511 provided a link below that has the raw data files. Here is the link for raw (CEL/CHP) data.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax57k

I did not realise the link i gave above is leading us to a completely different dataset.

I am looking for the data from GSE42133.

ADD REPLYlink written 2.6 years ago by aharnishi0270

How about this page. There are no CHP/CEL files though.

ADD REPLYlink written 2.6 years ago by genomax57k

Hi, could you tell me what does 'Raw data is available on Series record' mean?

ADD REPLYlink written 2.6 years ago by aharnishi0270

These are all the files that were submitted for this record. As I said before this does not appear to contain CHP/CEL files. Look in the "suppl" folder for the data labelled "raw". If you are after those then you will need to contact submitters.

ADD REPLYlink written 2.6 years ago by genomax57k

CEL files? If we are talking about the original dataset GSE42133, which author of the post is interested in, it is Illumina HumanHT-12 V4.0 expression beadchip, so the bead-level data should have TIFF extension (it's an image), while bead-summary level data - idat. And for some unknown reason people usually do not submit real raw data for Illumina.

"I had mailed the authors asking for the raw files, they reiterated that the raw files have been submitted and available online for download."

Do not want to offend the authors, but most probably they outsourced the analysis of raw data, and they could be unaware what is Illumina raw data exactly. Here is the rare case of when people uploaded idat files - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71625

So, I would suggest mailing authors again and explaining the situation.

And I recommend this package to deal with raw Illumina files - http://bioconductor.org/packages/release/bioc/html/beadarray.html

ADD REPLYlink modified 14 months ago • written 14 months ago by aln160
0
gravatar for mastal511
2.6 years ago by
mastal5112.0k
mastal5112.0k wrote:

If you navigate to the series record page,

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51808

And click on the options (http)(custom) under the Download heading at the bottom, there are a couple of ways to download raw data (CEL files).

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by mastal5112.0k

Hi,

Thanks for responding. But... Raw files in GEO are stored/uploaded with the following note: a) Raw data provided as supplementary file where the data is directly available for download which is what your link contains and there are no issues with that. b) Raw data is available on Series record and this is where i am facing a problem. I cannot access these files.

Could you help out with the series record

ADD REPLYlink written 2.6 years ago by aharnishi0270

Hi,

in the meanwhile did you get the raw data you were looking for? if yes could you please say how?

ADD REPLYlink written 16 months ago by H.Hasani610

If you are referring to the same record that @mastal511 had posted then the link for the raw data is at the bottom of the page and reproduced here.

ADD REPLYlink written 16 months ago by genomax57k

Not really, I was referring to his (b) question, if raw data was mentioned to be available, yet you can't find it...what to do

Raw data is available on Series record and this is where i am facing a problem. I cannot access these files.

ADD REPLYlink modified 16 months ago • written 16 months ago by H.Hasani610
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1522 users visited in the last hour