User: Yuya Liang

gravatar for Yuya Liang
Yuya Liang0
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Location:
Texas, USA
Last seen:
1 week, 6 days ago
Joined:
1 month ago
Email:
r********@tamu.edu

Posts by Yuya Liang

<prev • 8 results • page 1 of 1 • next >
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Comment: C: X-axis of MAplot and lfcShrink
... Thank you!! I got the result. ...
written 27 days ago by Yuya Liang0
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Comment: C: X-axis of MAplot and lfcShrink
... Thank you, Sir! I didn't notice it's 1e+05 instead of 1e-05. Do you happen to know lfcShrink( ) problem? ...
written 27 days ago by Yuya Liang0
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X-axis of MAplot and lfcShrink
... Hi everyone, The X-axis of my plot looks strange. Why the mean of normalized counts is super small? (My X-axis is 1e+01, 1e+05 but demo plot is 1, 100, 10000) Due to the shape of MA plot, I suppose to shrunk the log2 fold changes. I used lfcShrink() to do it but the result doesn't look like a outpu ...
deseq2 written 27 days ago by Yuya Liang0 • updated 27 days ago by Michael Love14k
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Comment: C: Strange MA plot
... Thank you so much, Dr. Love!!! I got the normal MA plot! ...
written 29 days ago by Yuya Liang0
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Comment: C: Strange MA plot
... I'm not sure if I did correct. I typed DESeq2::plotMA and checked `plotMA` my environment still shows . After that, I unloaded limma package by clicking "package" icon from right part of Rstudio but still got strang MA plot. The environment still . ...
written 29 days ago by Yuya Liang0
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Comment: C: Strange MA plot
... I got the following output when I typied plotMA in R. ``` > plotMA function (object, ...)  UseMethod("plotMA") <environment: namespace:limma> ```  Does it mean I was using limma package to plot? How to change it?   ...
written 29 days ago by Yuya Liang0
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Comment: C: Strange MA plot
...   Thank you for replying, Sir! The plot I post was the resulting plot when using the code plotMA(). I don't know if it's from DESeq2. And that's exactly my question. The plot doesn't look like the MA plot from the paper (RNA-seq workflow). I did library DESeq2 package and the same code but the plot ...
written 29 days ago by Yuya Liang0
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Strange MA plot
... Hi everyone, I got a strange MA plot like this: The code I used was simply like the manual: lncap_de <- DESeq(data_deseq_1) lncap_de_out <- results(lncap_de) res <- results(lncap_de, alpha = 0.05) plotMA(res) And, I checked the result by:​ head(res[ order(resSig$log2FoldCha ...
rnaseq deseq2 written 4 weeks ago by Yuya Liang0 • updated 4 weeks ago by Michael Love14k

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