User: g.wang2

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g.wang20
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Posts by g.wang2

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DESeq2 lfcShrink apeglm
... Thanks Michael. Yes, the version issue should be the reason. Currently run on a HPC with R/3.4.1., and previously on a local PC with a higher version of R. Thanks. ...
written 7 weeks ago by g.wang20
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DESeq2 lfcShrink apeglm
... Hello, I've been running DESeq2 recently using the lfcShrink function i.e. lfcShrink(dds, coef=14, type="apeglm", lfcThreshold=0.1375). However, an error was returned i.e. unused argument (lfcThreshold=0.1375). This has not occurred when I previously the same code above (some months ago). I'm wond ...
deseq2 written 7 weeks ago by g.wang20 • updated 7 weeks ago by Michael Love26k
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Low basemean and extremely high log2FC values, DESeq2
... Hello there, In a recent DESeq2 analysis, I've observed some low basemean values between 0.20 and 0.45 with the absolute log2FC values being around 20 or above in experimental conditions (i.e. Base2 vs Base1 and During 1 vs Base1 conditions) expecting no or small differences. I post below the summa ...
deseq2 interpretation written 10 months ago by g.wang20 • updated 10 months ago by Michael Love26k
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Comment: C: Handling missing data, DESeq2
... I post the entire colData here (masked) below for further evaluation, including 5 time points per subject for 10 subjects. Sample 40 (marked in bold) in S8 is dissimilar to all the rest of samples following the sample distance analysis. This observation is in line with what we expect given less volu ...
written 10 months ago by g.wang20
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Comment: C: how to handle missing data for SampleTable in DESeq2
... I see, thanks for pointing these out. I've now started a new post asking the question. Regards Guan ...
written 10 months ago by g.wang20
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Handling missing data, DESeq2
... Hello All, I've got some low quality RNA-seq data or data looking dissimilar in the sample distance analysis from a couple of samples that need removal. The samples were collected before, during and after a treatment. A question is - should the problematic samples be excluded only or the entire sub ...
deseq2 written 10 months ago by g.wang20 • updated 10 months ago by Michael Love26k
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Answer: A: how to handle missing data for SampleTable in DESeq2
... Hello there, I found this post tends to overlap with the question I'd like to ask, but not entirely. Therefore, adding the question here to this post: There're some low quality RNA-seq data or some data looking dissimilar in the sample distance analysis from a couple of samples that need removal. ...
written 10 months ago by g.wang20

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