User: -_-

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-_-610
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Posts by -_-

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Definition of transcript vs gene
... I am looking at GTF, and I see the figure below ![enter image description here][1] I wonder why these PCDH* (they share a single 3' end) are different genes rather than different transcripts of a single gene. [1]: https://image.ibb.co/djD3WJ/Screenshot_from_2018_05_11_10_50_49.png ...
gene transcript written 10 weeks ago by -_-610
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Comment: C: Subtyping on TCGA BRCA RNAseqV2 data with PAM50
... I've been thinking about this recently, for your information, here is what I've found, The PAM50 was actually first trained on qRT-PCR data, http://ascopubs.org/doi/full/10.1200/JCO.2008.18.1370, but this paper seems to have also used microarray data, together with qRT-PCR data, for clustering with ...
written 5 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... Quick question, please. How do people justify the adding of one, clearly it creates an artifact. I guess genes with a read size around one are just ignored, based on the d subplot of your attached image? ...
written 5 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... For the image, you need to click the image till you see a url ending with png or similar, e.g. http://image.ibb.co/dc7BYb/DESeq_Fig_S1.png. If you use Chrome, right click the image and then click Copy Image Address, then you will get the url. Great point, thank you! I will check the log transformat ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... This paper looks like just what I need, Thanks a lot! ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... Thanks. >If the assumption is true, the above data should be essentially a line because, at a given mean expression level, there is only one value for the variance, isn't it I didn't expect the relationship be to linear, either. It could be a non-linear line. I tend to agree with you. Do you m ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... Thanks. >in the absence of any data, if you guessed the average variance for genes of that expression level, you'd be right more often than anything else you could guess This is insightful. I need to read more about empirical bayes. It sounded very reasonable to me at first, but now given we h ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... Why would you only focus on the lower bound, then? If the assumption is true, the above data should be essentially a line because, at a given mean expression level, there is only one value for the variance, isn't it? Yes, [DESeq2][1] handles them separately >If, on the other hand, an individual ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... Wow. Thanks a lot for your detailed comment, really appreciate it! I agree with that all. I have no question that negative binomial deals with the overdispersion problem while Poisson assumes the mean and variance are always the same. But still, I am looking for other's opinion on the assumption beh ...
written 6 months ago by -_-610
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Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... @theobroma22, I don't think you are answering my question. I am not asking about negative binomial distribution at all. FYI, count data could have a Poisson distribution, too. Also, could you pinpoint what mathematical theory you are referring to? I recall modeling count data as negative binomial di ...
written 6 months ago by -_-610

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Scholar 13 months ago, created an answer that has been accepted. For A: How does deseq2 encode more than 2 levels
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