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 7 months 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 7 months 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 7 months 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 7 months 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 11 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 11 months ago by blastzone.heimerdinger0 • updated 11 months ago by Michael Love22k
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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 12 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 12 months ago by blastzone.heimerdinger0 • updated 12 months ago by Michael Love22k
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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 12 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 12 months ago by blastzone.heimerdinger0

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