User: blastzone.heimerdinger

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Posts by blastzone.heimerdinger

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Comment: C: The discrepancy between the mean of extracted fitted value and calculated mean a
... fittedval <- t( t( assays(results)[["mu"]] ) / sizeFactors(results) ) Thank you for the reply, and I'm sorry for the late response. I understand. If I somehow model (like linear model) the above fittedval data with my six independent variables, can I possibly reproduce the similar LFC? I wonder ...
written 9 weeks ago by blastzone.heimerdinger0
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Comment: C: The discrepancy between the mean of extracted fitted value and calculated mean a
... I understand, thank you very much!  Could you please tell me are there any way to extract fitted full model including other factors for the gene, so I can predict expression values considering other factors to reproduce LFC change? ...
written 9 weeks ago by blastzone.heimerdinger0
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Comment: C: The discrepancy between the mean of extracted fitted value and calculated mean a
... Hello, Thank you very much for the prompt help! I'm sorry now I can't show you the actual values of these, as I'm away from my workstation, but I have many other covariates like six, and I do not use LFC shrinkage. ...
written 9 weeks ago by blastzone.heimerdinger0
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
... Hello, I have a question regarding the discrepancy between the mean of extracted fitted value and calculated mean based on LFC.  First, I want to plot some of our fitted results in barplot, and I tried below code to extract fitted value and plot. fittedval <- t( t( assays(results)[["mu"]] ) / ...
deseq deseq2 written 9 weeks ago by blastzone.heimerdinger0
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Comment: C: Interpreting results of DESeq2, regarding baseMean and log2FoldChange.
... Thank you very much for the answer and pointing me to the right vignette! I read the section and still get confused about log2FoldChange ...  if I understand it correctly, ignoring the baseMean of all the samples displayed in the results() table, from the results we can conclude that "if baseMean of ...
written 6 months ago by blastzone.heimerdinger0
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Interpreting results of DESeq2, regarding baseMean and log2FoldChange.
... Dear forum,  Hello, I have a question regarding interpreting DESeq2 results regarding baseMean and log2FoldChange. I run DESeq() to perform differential expression analysis between group 1 and 2, and got the results like following, condition is c("1", "2").    baseMean log2FoldChang ...
deseq2 written 6 months ago by blastzone.heimerdinger0 • updated 6 months ago by Michael Love19k
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Comment: C: Normalized counts of DESeq2 affected by design formula?
...     Thank you very much for the reply! I want to do generalized linear modeling or mixed modeling for downstream analysis, for covariate adjusting, is it the case for using VST also? As I read that VST values should not be used to differential expression analysis. My intend is that I want deseq2 ...
written 7 months ago by blastzone.heimerdinger0
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Normalized counts of DESeq2 affected by design formula?
... Hello, sir. I have a question regarding normalized counts of DESeq2 (Not VST or rlog transformed). I used counts(normalized=TRUE) to get normalized data after DESeq() as follows.  norm_tbl <- counts(dds, normalized=TRUE) My question is that: 1. Can this normalized count table be used for do ...
deseq2 written 7 months ago by blastzone.heimerdinger0 • updated 7 months ago by Michael Love19k
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Comment: C: Using DADA2 output for DESeq2
... Thank you very much for the reply and clarity. This really answers my question. I will try first to do ASV-level testing. How great this forum is, to immediately got answers from actual developer of DADA2 and DESeq2! ...
written 7 months ago by blastzone.heimerdinger0
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Comment: C: Using DADA2 output for DESeq2
... Thank you very much for reply, and developing this wonderful package. ...
written 7 months ago by blastzone.heimerdinger0

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