User: cindy.perscheid

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New User
Location:
Hasso Plattner Institute, Potsdam, Germany
Website:
https://hpi.de/plattne...
Last seen:
47 minutes ago
Joined:
3 months ago
Email:
c**************@gmail.com

Posts by cindy.perscheid

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Multiple TCGA expression datasets
... As far as I know for the GDC, you can only query the data with parameters like study group, sample type, platform, and specific barcodes as the files are only available sample-wise (I suppose it is the same for all the other sources where you can download the data). I am afraid that you have to impl ...
written 50 minutes ago by cindy.perscheid30
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Comment: C: GDC TCGA Metadata no project ID available?
... Hi bharata, no, I have used TCGAbiolinks, who use the GDC API for querying. When downloading, they also get the metadata (the whole object is a SummarizedExperiment that contains both the expression counts and metadata) I can then access. Best, Cindy ...
written 5 days ago by cindy.perscheid30
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Data set with both genetic variants and gene expressions
... Hi there, as it seems getting access to the recently published GTEx data set (https://www.biorxiv.org/content/biorxiv/early/2016/09/09/074443.full.pdf; see discussion here https://www.biostars.org/p/283484/#283521) is quite hard for non-US institutions, I was wondering whether it is easier to just ...
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Comment: A: GDC TCGA Metadata no project ID available?
... As it here is only about a couple of barcodes with missing project_id, as we can look up the assigned study of them, and as we have no idea why this happens - I would now just try to fix the issue by manually filling in the project_id. Any concerns with this? Best, Cindy ...
written 6 days ago by cindy.perscheid30
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Comment: C: Experience with dbGaP controlled access from outside the US?
... Thanks for the hint. It turns out we already have a DUNS number, so I will probably give it a try. When I read about all the other web pages for registration and always just saw "US government" and "grants" I had the impression that it is not possible for non-US-granted institutions at all. Good to ...
written 6 days ago by cindy.perscheid30
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Comment: C: Experience with dbGaP controlled access from outside the US?
... Genomax, thanks a lot for the link. I had to laugh really really hard. Currently, I am kind of outraged at the same level. ...
written 6 days ago by cindy.perscheid30
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Comment: C: GDC TCGA Metadata no project ID available?
... Hi Kevin, yes - I mean the study type when talking about project_id (this is the attribute in the colData in which it is encoded). Currently, I have 6 samples with no study type. Some of them are normal tissues (TN), some of them cancer tissues (TP). I cannot really find any pattern here. Additional ...
written 6 days ago by cindy.perscheid30
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Experience with dbGaP controlled access from outside the US?
... Hi there, I want to get controlled access to dbGaP - in particular to the data that is linked here (section: "Download from dbGaP"): https://github.com/joed3/GTExV6PRareVariation I am based at the University of Potsdam, Germany and hence have none of the accounts requested for application (eRA Co ...
controlled access dbgap written 6 days ago by cindy.perscheid30 • updated 6 days ago by i.sudbery1.7k
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GDC TCGA Metadata no project ID available?
... Hi there, I recently downloaded data from the GDC, and to keep track of which sample belongs to what study and have which sample type, I also created a small metadata file. However, it seems that some of the samples do not have a study type assigned - or I must have a strange side effect in my scri ...
gene expression metadata tcga gdc written 6 days ago by cindy.perscheid30
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Comment: C: Can I use TCGA FPKM-UQ values directly to compare across samples without any pre
... I do agree with Kevin. There was a paper in 2012 comparing the state of the art normalization techniques, and it stated that RPKM/FPKM should not be used and DESeq2 and TMM worked best. Have a look at the paper: https://academic.oup.com/bib/article/14/6/671/189645/A-comprehensive-evaluation-of-norma ...
written 6 days ago by cindy.perscheid30

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