User: Vasei

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Vasei20
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20
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1 week ago
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2 years, 7 months ago
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Posts by Vasei

<prev • 11 results • page 1 of 2 • next >
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TCGA metastatic samples
... I downloaded clinical data of BLCA and BRCA cancers from [firebrowse][1] which provides an easy way to access TCGA project's data. Using sample barcodes with sample type code "06"(according to [this link][2]), I could not find any metastatic samples. I also tried to use [GDC Data Portal][3] to find ...
tcga written 9 weeks ago by Vasei20 • updated 6 weeks ago by Kevin Blighe28k
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(Closed) Why cancer is more lethal than (hypothetical)infections?
... I don't know is here the right place to ask this question but I think the community is the right community to answer my question! I am a computer science student and I'm interested in algorithmic aspects of cancer! Once I heard that there exist more bacteria in human body than our own cells, I wond ...
bacteria cancer written 9 months ago by Vasei20
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samr package for Significance analysis of microarrays, SAM function resp.type parameter
... What is default behavior of `SAM` method when we do not specify `resp.type` parameter? ...
R sam samr written 2.0 years ago by Vasei20 • updated 22 months ago by Biostar ♦♦ 20
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Answer: A: TCGA microarray comparison with RNA-seq
... I found the answer to my own question! The microarray platform that I mentioned is a two channel microarray and the answer is stated in [Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data][1]: > The low Spearman correlation between the two-channel microarr ...
written 2.1 years ago by Vasei20
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Answer: A: How to calculate "fold changes" in gene expression?
... Fold change can also be computed in unsupervised fashion, where we don't know the class labels(like case-control or type1-type2) of the samples. In that setting we can use mean expression of a gene as the base value and compute the fold change for that gene in each sample. ...
written 2.1 years ago by Vasei20
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TCGA microarray comparison with RNA-seq
... I downloaded microaaray and rna-seq data for breast cancer of the TCGA project from the [firehose][1] portal. When I computed the correlation between expression of each gene in different patients, correlation was high, as I expected. Correlation mean was 0.65 and median was 0.75. Intrestingely there ...
tcga microarray breast cancer rna-seq written 2.1 years ago by Vasei20
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Comment: C: Why there are genes that are not present in TCGA normalized rna-seq data?
... Thank you. That sounds completely correct. ...
written 2.4 years ago by Vasei20
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Comment: C: Very basic for a student: How to analyse RPKM expression data to identify genes
... I think details here are not so important. You have 11000 samples of hypothesis testing problem. Using simple tests like t-test can be useful! I emphasis that I agree with @decosterwouter that you must not compare just average values and should use variation in the samples. There exists advanced m ...
written 2.4 years ago by Vasei20
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Comment: C: Why there are genes that are not present in TCGA normalized rna-seq data?
... Thanks. I think that data is not filtered because there are many genes with 0 reads across many samples and also there are exactly 20532 genes in all the cohorts. I will take a look at preparation methods, but I think both of them are using polyA filtering and measuring mRNA levels. ...
written 2.4 years ago by Vasei20
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Why there are genes that are not present in TCGA normalized rna-seq data?
... I was doing a comparison between gene expressions for TCGA data obtained from microarrays and rna sequencing. I downloaded normalized data from [firebrowse][1] and when comparing gene names in those two platforms, I noticed that there are nearly 1000 genes that are present in microarray data but not ...
tcga rna-seq written 2.4 years ago by Vasei20 • updated 2.4 years ago by Jordan Anaya920

Latest awards to Vasei

Popular Question 5 months ago, created a question with more than 1,000 views. For TCGA microarray comparison with RNA-seq
Popular Question 8 months ago, created a question with more than 1,000 views. For TCGA microarray comparison with RNA-seq
Scholar 2.1 years ago, created an answer that has been accepted. For A: TCGA microarray comparison with RNA-seq

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