User: hougiotaejut

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hougiotaejut10
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Posts by hougiotaejut

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Normalization methods in RNA-seq read counts data
... Thanks a lot for your response. I noticed that the first one is the ratio of medians while the second one is median of ratios. I still feel a little confused as you say these are the same. I guess they give different amounts when applied on data. because if you, first, obtain the median of counts ac ...
written 10 weeks ago by hougiotaejut10
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Comment: C: Normalization methods in RNA-seq read counts data
... Thanks a lot. I was trying to fix it then I saw you did the favor to me. ...
written 10 weeks ago by hougiotaejut10
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Comment: C: Normalization methods in RNA-seq read counts data
... Thank you. Yeah I was trying to fix it when I saw they weren't shown. ...
written 10 weeks ago by hougiotaejut10
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Normalization methods in RNA-seq read counts data
... Hi there is a paper where the writer claims that they have implemented "Median", "Quantile", "TMM" and "Total" normalization methods in their R package. But I don't find their normalization methods similar to those being referenced. For example, the library size estimation in "Median" normalization ...
differential analysis written 10 weeks ago by hougiotaejut10 • updated 10 weeks ago by Devon Ryan84k
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Comment: C: Make artificial read count table
... I wanted to know if I understand that paper correctly. That's why I asked my question here. Because it seemed so strange to me to just copy and replace the replicates. ...
written 12 weeks ago by hougiotaejut10
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Make artificial read count table
... Hi, Assume that you have a count table where there are two dependent conditions with 3 replicates each. Gene R1-C1 R2-C1 R3-C1 R1-C2 R2-C2 R3-C2 X1 43 52 38 120 131 115 X2 250 273 ...
simulation artificial rna-seq written 12 weeks ago by hougiotaejut10 • updated 12 weeks ago by h.mon19k
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Comment: C: Heatmaps: Why and How to use them
... After scaling the normalized counts, my heatmap has changed significantly. ...
written 20 months ago by hougiotaejut10
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Comment: C: Heatmaps: Why and How to use them
... One of the models provides me with the log2fold changes and p-values, but the other one doesn't. So I don't know how to further filter the DEGs by log2fold change for the second model. it only gives me the DEGs, and their PPs (posterior probabilty). and thanks for mentioning the code above. I took ...
written 20 months ago by hougiotaejut10
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Comment: C: Heatmaps: Why and How to use them
... Thank you very much. I'm trying to compare two models. So I haven't changed the default settings for each model and that is why they give me a high number of DE genes. I want to figure out how close these two models work by default by comparing their results on finding the index genes and their numb ...
written 20 months ago by hougiotaejut10
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Comment: C: Heatmaps: Why and How to use them
... Thank you very much for the info ...
written 20 months ago by hougiotaejut10

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Popular Question 6 months ago, created a question with more than 1,000 views. For Heatmaps: Why and How to use them

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