User: atakanekiz

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atakanekiz70
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Posts by atakanekiz

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Significant but very small beta coefficients in Cox proportional hazards calcula
... I found out what the problem was. My gene expression data were in linear scale. When I transformed it to log scale, hazard values appeared more like what I expected. P-values were also an order of magnitude smaller due to lower variation in log-scale. Hopefully this will be helpful for somebody hav ...
written 8 weeks ago by atakanekiz70
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Significant but very small beta coefficients in Cox proportional hazards calculation (survival)
... Hello CV community, I'm analyzing TCGA data to investigate the effects of lncRNAs on survival. Among other things, I wanted to calculate a univariate CoxPH model for each gene to find genes whose expression levels have a significant correlation with survival outcome. I realize that I'm not testing ...
cox survival analysis survival rna-seq hr written 8 weeks ago by atakanekiz70
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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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by atakanekiz70

Latest awards to atakanekiz

Scholar 8 weeks ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
Scholar 3 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data

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