User: boaty

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boaty90
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Posts by boaty

<prev • 27 results • page 1 of 3 • next >
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Comment: C: How to make differential expression analysis with normalized data?
... look at this first [tximport][1] tximport will take normalised count and length information to recompute raw count...... you can use tximport to get pseudo raw count then use deseq2 for GDE It works for almost all the modern count quantification tools like kallisto, stringtie. But you need to know w ...
written 10 weeks ago by boaty90
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Comment: C: How to make differential expression analysis with normalized data?
... which tool is used for quantification? RSEM, stringtie, cufflink? just try tximport package from deseq2 team ...
written 10 weeks ago by boaty90
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Answer: A: Why I have too many reads non uniquely aligned?
... Hi, I think it's fine, depends on what kind of analysis you want to perform? Here the main question is, do you have enough read depth or statistical power to do a GDE? you have 23M reads out of aligner and 10M of them are not unique so 13M unique reads for analysis. I think it's OK for GDE. RNA-s ...
written 10 weeks ago by boaty90
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Comment: C: concern about statistical model after more than 78% of genes are differentially
... thanks again. the experiment will give us insight of what gene's transcript will concentrate in that organelle. So here comes my concern, Deseq2's pvalue from nbinomialWaldtest() is key for filtering genes but if Desqe2 statistical model is not fit for my data, those p value will misguide the selec ...
written 4 months ago by boaty90
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Comment: C: concern about statistical model after more than 78% of genes are differentially
... thank you I just updated my question, it will answer your question ...
written 4 months ago by boaty90
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Comment: C: concern about statistical model after more than 78% of genes are differentially
... thanks I modified my text, the comparison is between cytosol droplet organelles RNA and all RNA in cytosol. So in droplet, a small part of RNA will be enriched. my concern is that the stats model build by Deseq2 will not fit this data and give more false negative. ...
written 4 months ago by boaty90
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Comment: C: What to do if more than 78% of genes are differentially expressed according to D
... thanks I modified my text, the comparison is between cytosol droplet organelles RNA and all RNA in cytosol. So in droplet, a small part of RNA will be enriched. my concern is that the stats model build by Deseq2 will not fit this data and give more false negative. ...
written 4 months ago by boaty90
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Comment: C: What to do if more than 78% of genes are differentially expressed according to D
... thanks. the extraction will extract Droplet-Like Organelles in cytosol which only some special RNA is enriched. This is not a conventional DE, I am not comparing the expression between different times or different conditions. the comparison is between RNA in Droplet_like Organelles and all RNA in c ...
written 4 months ago by boaty90
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concern about statistical model after more than 78% of genes are differentially expressed according to DESeq2?
... Hi guys, I got a RNA-seq data from the extraction of cellular droplet. Thanks to extraction method, a fraction of cytosol material : droplets, mixed with RNA and protein are separated from the whole cytosol. And now I want to do a comparison between all RNA in cell and RNA present in droplet like ...
rnaseq deseq2 written 4 months ago by boaty90
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Comment: C: any idea about histogram(graphic) clustering?
... thank you very much. the dynamic time warping and wasserstein distance are exactly what I am searching for. and converting frequency hist to probability density distribution is just genius. thanks again. ...
written 5 months ago by boaty90

Latest awards to boaty

Supporter 4 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: guidance for communication online seach engine with python or R script?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: guidance for communication online seach engine with python or R script?

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