User: rGun

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rGun10
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7 months ago
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Posts by rGun

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DEG analysis of METABRIC data from cBIOPORTAL
... It says data_expression_median.txt and a representative summary of data distribution for a sample looks like below; Min. 1st Qu. Median Mean 3rd Qu. Max. 4.713 5.401 5.659 6.423 7.095 14.464 whereas for the same sample in the z-score file (data_mRNA_median_Zscores.txt) summa ...
written 7 months ago by rGun10
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Comment: A: DEG analysis of METABRIC data from cBIOPORTAL
... Any idea on what the median data file that comes along with the download? Thanks! ...
written 7 months ago by rGun10
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Comment: A: DEG analysis of METABRIC data from cBIOPORTAL
... Thanks, Kevin. I checked the distribution of data for each test category and they looked normally distributed.I did ANOVA and Kruskal-Wallis ANOVA on z-scores. Just wanted to make sure that I didn’t missing any. Also, thanks again for your answer on implementing K-W and parametric ANOVA in R. It was ...
written 7 months ago by rGun10
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DEG analysis of METABRIC data from cBIOPORTAL
... I downloaded expression (microarray), clinical and mutation data associated with METABRIC breast cancer study from cBIOPORTAL and I'm planning to analyze the dataset for DEGs among three subsets of individuals, subsetted based on a mutational status. I'm not familiar with using median and z-score ex ...
R deg analysis cbioportal breast cancer written 7 months ago by rGun10
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Comment: C: Association study using germline SNPs, somatic mutations in tumors and clinical
... Thanks for the information! I really appreciate it. I have some experience in analyzing datasets but this will be my first venture into TCGA data. However, the clinical correlations with a SNPs will be done by our collaborator. I'd really appreciate if you could direct me to any similar study that y ...
written 2.2 years ago by rGun10
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Comment: A: Association study using germline SNPs, somatic mutations in tumors and clinical
... Thanks a lot, Kevin. We have already done a study where we looked at association between SNPs/certain haplotypes with increased risk for BrCa. We wanted to see whether our findings will hold in another similar dataset. Since we are in the process of getting access to restricted TCGA data, I thought ...
written 2.2 years ago by rGun10
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Association study using germline SNPs, somatic mutations in tumors and clinical data from TCGA
... Hi all, I'm interested in doing an association study using germline SNPs of specific pathways, tumor mutations and clinical data from a patient population in TCGA. I'm currently in the process of getting access to the datasets. If anyone has experience with this type of a study, any advice on how I ...
tumor mutations tcga snp clinical data written 2.2 years ago by rGun10

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