User: atakanekiz

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atakanekiz70
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Posts by atakanekiz

<prev • 8 results • page 1 of 1 • next >
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Answer: A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... Hi Matina, I would go with the `days_to_death` and `days_to_last_follow_up` (for alive patients) for survival analyses. I think stuff that starts with `subtype_` might be manually curated data. I'm not 100% sure but, `subtype_OS.Time` sounds like the time period that the tumor was classified as a c ...
written 12 days ago by atakanekiz70
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Answer: A: Differences between RTCGA and TCGAbiolinks data
... Alright, I think I figured out what's going on. The biggest difference in the results was caused by a missed point during pre-processing. Please see below: `RTCGA` features an already preprocessed data frame with clinical parameters. In this data frame there is a `times` variable that combines bo ...
written 12 days ago by atakanekiz70
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Comment: C: error in GDCprepare
... Hi, This is a bit of a late follow-up, but I'm running into the same problem with `TCGA-SKCM` legacy `miRNA gene quantification` data. Have you been able to solve your problem? If yes, can you please share how? Best, Atakan ...
written 12 days ago by atakanekiz70
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Answer: A: Differences between RTCGA and TCGAbiolinks data
... Today I met with few bioinformaticians at my institute and got some good suggestions. I will perform more analyses to fully understand what's going on but as a summary: 1) The main difference is potentially caused by the utilization of harmonized data (via `TCGAbiolinks`) vs legacy data (from `RTCG ...
written 13 days ago by atakanekiz70
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Hi svlachavas, Yes I think the main difference between `RTCGA` datasets and the ones acquired with `TCGAbiolinks` is that the former has the legacy version whereas the latter pulls out the most recent harmonized data from GDC. I will run the analyses with legacy data by using TCGAbiolinks and updat ...
written 13 days ago by atakanekiz70
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Hi Efstathios-Iason, Great questions. Let me answer as much as I can: 1) TCGAbiolinks package fetched the `harmonized` data but I'm pretty sure `RTCGA` uses legacy data (from 2015-11-01 release). I knew this would potentially introduce variation, but didn't expect it would be this big. 2) Yes in ...
written 13 days ago by atakanekiz70
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Hi Kevin, Thank you for your answer. This was along the same lines as what I was thinking. The data of `RTCGA` is from `2015-11-01`snapshot. If I'm understanding correctly, `TCGAbiolinks` downloads the most updated data directly from GDC. I used the harmonized data instead of the legacy version fr ...
written 13 days ago by atakanekiz70
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Differences between RTCGA and TCGAbiolinks data
... Hello Biostars community, I'm trying to analyze miRNASeq data of TCGA melanoma (SKCM) samples. This is a prototype analysis in which I picked `hsa-mir-155` and looked at how its expression is correlated with survival. My end goal is expanding this analysis to other cancer types also focusing on oth ...
R mirnaseq survival analysis rna-seq written 13 days ago by atakanekiz70

Latest awards to atakanekiz

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
Scholar 12 days ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data

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