User: 2002ymx02

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2002ymx020
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Posts by 2002ymx02

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Comment: C: Applying norm.factors in RNA-seq analysis to other expression data by using edge
... Many thanks. Now I understand why norm.factors is data-specific. The aim of calcNormFactors function to adjust expressions in each samples to a level at which all samples are comparable by norm.factors*lib.size. If I use a fixed norm.factors, then the normalized data are still uncomparable, because ...
written 21 days ago by 2002ymx020
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Comment: C: Applying norm.factors in RNA-seq analysis to other expression data by using edge
... Thank you, Gordon. I think the read depths are the same. Even the library composition could be different, but the trimmed mean could be similar. So I supposed using the same norm.factors could be good. If I run separate calcNormFactors function on each expression data, I could get different norm.fa ...
written 21 days ago by 2002ymx020
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Comment: C: Applying norm.factors in RNA-seq analysis to other expression data by using edge
... Thank you for your time, Gordon. Maybe I was not clear in my question post. These different expression data are actually from the same samples and from same sequencing files (.fasta). I just got the different expression data by using different aligners to different genomic regions for specific le ...
written 21 days ago by 2002ymx020
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Applying norm.factors in RNA-seq analysis to other expression data by using edgeR
... Hi edgeR authors, I would like to apply the norm.factors calculated in gene expressions by using edgeR pipeline to other expression data, for example small RNA and transposon expression in the same samples. After puting counts and group into DGEList object, I assigned norm.factors to samples$norm.f ...
edger written 21 days ago by 2002ymx020 • updated 21 days ago by Gordon Smyth38k
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Comment: C: The meaning of interaction terms in design matrix in edgeR User's Guide on page
... Many thank, Gordon. Yes, they are the same. ...
written 8 weeks ago by 2002ymx020
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Comment: C: The meaning of interaction terms in design matrix in edgeR User's Guide on page
... Thank you for your time, Gordon. Actually, my understanding of interaction terms [5] "TreatDrug:Time1h", [6] "TreatDrug:Time2h" are (Drug.1h-placbo.1h)-(Drug.0h-placebo.0h) and (Drug.2h-placbo.2h)-(Drug.0h-placebo.0h) respectively, which are different from the definition on page 36 of the Guide: D ...
written 8 weeks ago by 2002ymx020
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The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
... Hi Prof. Gordon Smyth, I have a question about the meaning of interaction terms in design matrix on the page 38 in the edgeR User's Guide. In line 19, the guide say: "The last two coefficients give the DrugvsPlacebo.1h and DrugvsPlacebo.2h contrasts". But my understanding is that the last two coe ...
edger written 8 weeks ago by 2002ymx020 • updated 8 weeks ago by Gordon Smyth38k
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Comment: C: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
... Thank you Prof. Gordon for your reply. ...
written 8 weeks ago by 2002ymx020
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Comment: C: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
... Thank you for your edgeR and imma. Here is another typo: it shoud be CvsA=C-A, not CvsA=A-C in the last second line on page 31. And it could be better to say: .....genes that are always "significant" in red cells, not always "higher" in last line 6 on page 32, because for DE analysis, the first r ...
written 8 weeks ago by 2002ymx020
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Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
... Hi Gordon Smyth and other authors of edgeR, It seemed that the colnames of design2 on page 34 in edgeR User's Guide were wrong. They should be (intercept), groupA and groupB, not (intercept), groupB and groupC, because groupC was releveled as reference. Could you check this? Best, Mingxing Yang ...
edger written 9 weeks ago by 2002ymx020 • updated 8 weeks ago by Gordon Smyth38k

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