User: ebrudermanver

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Posts by ebrudermanver

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Diseased tissue gene expression source
... I know that there are many sources such as GTex or Human Protein Atlas that provides information about whether a gene is expressed in a tissue. Is there a similar source which shows how much a gene is expressed in **diseased tissues** ? ...
gene expression disease written 7 months ago by ebrudermanver60 • updated 7 months ago by Denise - Open Targets5.1k
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Genes that affect cancer prognosis in general
... Is there something like *cancer survival pathway*, or *cancer prognosis pathway* that lists genes that are generally impacting how long people with cancer live. I am looking for a canonical pathway or a GO term, similar to the set of ~300 genes in KEGG_PATHWAYS_IN_CANCER, but specifically for progno ...
gene survival cancer written 22 months ago by ebrudermanver60
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Comment: C: Difference between DNA microarray and RNA microarray
... "We use the term RNA microarrays to refer to arrays used to measure RNA levels, whereas DNA microarrays measure DNA sequence or levels." --- This statement from a book pops up when you search for -"dna microarray" vs "rna microarray"- on Google. I think it is always a DNA microarray, but the naming ...
written 2.2 years ago by ebrudermanver60
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Comment: C: Difference between DNA microarray and RNA microarray
... This response is not replying to my question, unfortunately. What I asked is the difference between DNA microarray and RNA microarray. Both of those are array sequencing methods, while RNA-Seq is something totally different. ...
written 2.2 years ago by ebrudermanver60
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Difference between DNA microarray and RNA microarray
... What is the technological differences between the DNA microarray and RNA microarray, specifically when gene expression is measured by each? Wikipedia says "Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a ge ...
gene sequencing written 2.2 years ago by ebrudermanver60 • updated 2.2 years ago by Aerval280
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Comment: C: Calculating FPKM values from HT-counts
... Hi Devon, could you please explain a little more why is it best not to convert raw RNASeq counts to FPKM values? You also said "if you want to compare between samples, that you should use normalized counts, since FPKMs made from raw counts are inappropriate for comparison between samples"; what does ...
written 2.3 years ago by ebrudermanver60
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Comment: C: What does it mean to model expression data by a probability distribution?
... So, relating this to my actual question, are you saying that each column (gene) in the example I gave is distributed by a Gaussian distribution? Why not each row (sample)? ...
written 2.5 years ago by ebrudermanver60
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What does it mean to model expression data by a probability distribution?
... I have very frequently seen in the papers, lecture notes etc. that RNA-Seq data can be modeled by a Poisson distribution, and microarray data can be modeled by a Gaussian distribution, and I haven't given much thought on that. But I recently realized that I don't really understand what that means. L ...
rna-seq distribution microarray written 2.5 years ago by ebrudermanver60 • updated 2.5 years ago by Jean-Karim Heriche21k
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Answer: A: What is the reason why we usually use normalized values from RNA-Seq (FPKM, RPKM
... Okay, I just found [that link][1] which says that FPKM makes it possible to compare Gene A to Gene B even if they are of different lengths, and to compare Sample 1 and Sample 2 even if they have different library sizes. [1]: http://www.cureffi.org/2013/09/12/counts-vs-fpkms-in-rna-seq/ ...
written 2.5 years ago by ebrudermanver60
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What is the reason why we usually use normalized values from RNA-Seq (FPKM, RPKM, etc.) ?
... I don't have much experience with RNA-Seq but I am seeing that the data is usually published not in raw counts but in FPKM values. What is the reason for that? Is it only because so that we can model the values by a log-Gaussian distribution rather than a discrete distribution like Poisson or negati ...
rna-seq written 2.5 years ago by ebrudermanver60 • updated 2.5 years ago by Michael Dondrup47k

Latest awards to ebrudermanver

Popular Question 22 months ago, created a question with more than 1,000 views. For PLINK linear association
Popular Question 22 months ago, created a question with more than 1,000 views. For Using PLINK to check SNP variation for a gene
Popular Question 22 months ago, created a question with more than 1,000 views. For RNA-Seq data distribution
Popular Question 22 months ago, created a question with more than 1,000 views. For Difference between DNA microarray and RNA microarray
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Using ComBat on RNASeq FPKM counts

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