I have encountered the same problem on GSE111368, there is no raw data there. Previously, the person in charge of uploading it insisted that the raw data was uploaded and was there. After I reported the issue to the editor of nature immunology, he finally admitted that the raw data is not available on the GEO website. However, he refused to share the raw data and claimed that per the requirement of GEO they are responsible to share raw data. Then I sent an email to GEO to check it since I saw that the raw data is required by GEO. Then GEO responded that they do accept non-normalized data in tabular format as an alternative to IDAT files.
To those who face the same problem, this should let them know why people don't give raw data from the beadarray.
This is the message from the uploader.
As per requirement from GEO, we do not have to upload .idats file anymore because it’s too large. The non-normalised data from GEO is good enough for you to start the analysis from beginning. It has raw intensity signals and detection P values.
L
This is the message from the GEO team.
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ORIGINAL CC line was: tirouvan@gmail.com, dmoncad@emory.edu
Dear Chunhui,
To be clear, we do accept non-normalized data in tabular format as an alternative to IDAT files. That said, we have written to the submitters of
GSE111368 to encourage them to add the IDAT files.
We will inform you upon receiving their response.
Best Wishes,
The GEO Team
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Does not look like the raw data is available for this accession.
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?
@mastal511 provided a link below that has the raw data files. Here is the link for raw (CEL/CHP) data.
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.
How about this page. There are no CHP/CEL files though.
Hi, could you tell me what does 'Raw data is available on Series record' mean?
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.
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