User: Vasei

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Vasei20
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Posts by Vasei

<prev • 13 results • page 1 of 2 • next >
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Where to find location of sequenced exons in TCGA whole exome sequencing data
... I want to analyze mutation distribution among the exons using MAF files from TCGA project. For this purpose I need to know the location of sequenced exons. Is there an easy way to find these locations? Do center which performed sequencing and sequencer technology determine these locations? ...
tcga cancer sequencing written 13 days ago by Vasei20
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Answer: A: How To Compute The Significance Of The Overlap Of The Size Of The Intersection O
... You can use resamplin (sometimes called permutation test) in this case. Assuming your gene list is L, you can sample A of size 80 and B of size 45 independently from L, and see if the size of intersection is more or less than 15. By repeating this many times you get an estimate of probability of an ...
written 27 days ago by Vasei20
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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 4 months ago by Vasei20 • updated 3 months ago by Kevin Blighe32k
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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 11 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 2.2 years ago by Vasei20 • updated 2.0 years 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 2.2 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 2.2 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 2.3 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 2.6 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 2.6 years ago by Vasei20

Latest awards to Vasei

Supporter 11 days ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For TCGA microarray comparison with RNA-seq
Popular Question 10 months ago, created a question with more than 1,000 views. For TCGA microarray comparison with RNA-seq
Scholar 2.2 years ago, created an answer that has been accepted. For A: TCGA microarray comparison with RNA-seq

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