Comments (5)
Thank you for pointing this out. We were aware that there were occasional cases when this happened, but did not know there were so many of them. We will re-run these.
I am curious, how did you compile the list? Is this an exhaustive list of datasets with this problem, of they are just datasets that you were interested in and they happened to be problematic?
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@Mario-Medvedovic Thank you for your reply! I am an oncologist and I am currently systematically searching for RNA data of tumors. My search criteria include: 1) human solid tumor tissue, 2) bulk RNA-seq, and 3) data from 2009 onwards. I have checked the number of datasets available from the 171 included studies and have compiled the list above. Although I only need four of them, I thought it would be appropriate to report all of them to you.
By the way, this platform is very helpful, and I have recommended it to my colleagues. They all agree.
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Thank you for info. As I said, I will re-run these. I will also run a comprehensive check over all datasets. It is very gratifying to hear that somebody like yourself finds GREIN useful.
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All datasets in the list above have been re-processed now, and all except one (GSE184336) are available in GREIN. For GSE184336, our pipeline failed in extracting fastq files. We intent to troubleshoot, but this may take a while.
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@Mario-Medvedovic Thank you for the update on the reprocessing of the datasets. It was completed much faster than expected, and it has already helped a lot. There isn't much I could help, I will continue to report any bugs I encounter in the future as a form of support. Thank you again!
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Related Issues (20)
- website down? HOT 3
- Analysis not done HOT 2
- All counts are zero HOT 1
- Gene number different from different dataset HOT 2
- Combine multiple dataset from GREIN HOT 2
- Duplicated gene symbol HOT 2
- GEO_data_processing.R get error
- GEO_data_processing error
- Site not loading HOT 2
- SIte not loading (bis) HOT 1
- new datasets HOT 3
- ALL SAMPLES ARE NOT INCLUDED FOR ANALYSIS HOT 2
- Count table at gene level HOT 7
- Hi. I downloaded raw counts for GSE83577, but the data corresponds to normalized counts. Is this a problem just for this dataset of a platform bug? thanks
- Any possibility for mass download or API for dataset HOT 1
- Incomplete Dataset and New Datasets HOT 4
- Some datasets are not loading completely
- Fast download of Count Matrix? HOT 2
- ERROR: GSE174836 cannot be processed HOT 1
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