User: Yuya Liang

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Yuya Liang0
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r********@tamu.edu

Posts by Yuya Liang

<prev • 26 results • page 1 of 3 • next >
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Comment: C: The calculation of regularized logarithm
... I will read them again more carefully. Thank you for explaining everything! ...
written 5 months ago by Yuya Liang0
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Comment: C: The calculation of regularized logarithm
... Thank you for bringing this out again! I didn't express this clearly. I guess "Not recommend to use vst or rlog for statistical analysis of LFCs per gene" meaning not use the rlog counts for comparing control and treatment.  If rlog is not helpful for solving βir, why formula (2) we put rlog inste ...
written 5 months ago by Yuya Liang0
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Comment: C: The calculation of regularized logarithm
... Thank you so much!! So I can just simply say that this difference between raw count and rlog count due to "counts in all samples were moved toward the center(middle)" and this will help to calculate distances, correct?  (also help to calculate coefficient as well?) ...
written 5 months ago by Yuya Liang0
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Comment: C: The calculation of regularized logarithm
... Can you give me some information for why rlog makes raw counts from zero to non-zero? I expected to see huge different in this kind of extremely opposite (i.e. zero vs. some counts) but not. Even the rlog counts were not that different, they still got large LFC and significant pdaj. I'm just curiou ...
written 5 months ago by Yuya Liang0
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Comment: C: The calculation of regularized logarithm
... Got it!  I found a previous reply https://support.bioconductor.org/p/64014/#64016. Is this the reason why sample with 0 raw counts will have the value greater than 0?  ...
written 5 months ago by Yuya Liang0
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Comment: C: The calculation of regularized logarithm
... Thank you for replying! It helps a lot. I have two more questions:  This is the formula I cropped from DESeq2 paper:                          The log_qij for solving βir is the value from rlog(), is that correct? (I'm not sure is log2 or log10.)       2.   I also found a formula in the above ...
written 5 months ago by Yuya Liang0
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The calculation of regularized logarithm
... I was wondering (1) how does rlog( )calculate values from raw counts, (2) the relationship between rlog counts and the effect estimator (βir), and (3) what information rlog counts tell.   In vignette:                     log2(qij) = Xj βi Q1: Is log2(qij) here represent the values from rlog  ...
rnaseq deseq2 written 5 months ago by Yuya Liang0 • updated 5 months ago by Michael Love20k
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Comment: C: Compare effect size of gene (lfcShrink or not)
... I saw it... Thank you!! ...
written 5 months ago by Yuya Liang0
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Comment: C: Compare effect size of gene (lfcShrink or not)
... It seems not too much different. Is that normal? This is the code I used: ​ DESeq.A <- DESeq(DESeq.ds, test = "Wald") a <- results(DESeq.A) resLFC <- lfcShrink(DESeq.A, coef = 2, res = a, type = "normal") resLFC.ape <- lfcShrink(DESeq.A, coef = 2, res = a, type = "apeglm") par(mfrow ...
written 5 months ago by Yuya Liang0
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Comment: C: Compare effect size of gene (lfcShrink or not)
... Thank you! It works. ...
written 5 months ago by Yuya Liang0

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