User: sum732

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sum7320
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Posts by sum732

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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael. I will into stageR and ImpulseDE2.  ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael as suggested I will and perform pairwise analysis and then look at stageR.  One thing that is still confusing me was when I did performed LRT test as you had suggested. Why did the comparisons was with age12M?  [1] "Intercept"      "Age_M18_vs_M12" "Age_M21_vs_M12" "Age_M6_vs_M12" ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael and apologies for any confusion.  Perhaps restating will be helpful.  I have samples with replicates for diff time periods (age) and no condition. I want to perform DGE and capture genes that have changed across the ages. Use of LRT was suggested ddsMat_MouseAge<-DESeqDataSetFr ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael for the response. I do get the part of seeing a single coefficients and use of name in results to get the LFC, p and q among other stats. The values shown must be element of resultsNames(object). Looking at the output from resultsName, the comparison is against M12. This is after us ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Simon, But "18M", "12M"  etc should be level? and from  ​resultsNames(dds) We know they are not. Only following are:  "Age_M18_vs_M12" "Age_M21_vs_M12" "Age_M6_vs_M12"  ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Hi Michael, As suggested: dds<-DESeqDataSetFromMatrix(MouseAge,expSummary_MouseAge,~Age) dds <- DESeq(dds, test="LRT", reduced=~1) design(dds) results(dds) resultsNames(dds) res <- results(dds) Using ​resultsNames(ddsMat_MouseAge) I can see the comparisons performed. [1] "Intercept"   ...
written 4 weeks ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael for a prompt response.  I had tried something similar after reading your suggestion given here (with modifications): https://support.bioconductor.org/p/63201/ ddsMat_MouseAge<-DESeqDataSetFromMatrix(MouseAge,expSummary_MouseAge,~Age) ddsMat_MouseAge <- DESeq(ddsMat_MouseAge ...
written 4 weeks ago by sum7320
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Answer: A: DESeq2 Time Series and "control" condition
... Sorry wrong window and cannot delete the "comment post above" ...
written 4 weeks ago by sum7320
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DESeq2 Time Series and "control" condition
... Hello, I am trying to perform DGE analysis for a time series data. I am using DESeq2 for the analysis.  Upon searching the closes match I can get to what I am trying to do is here: http://seqanswers.com/forums/showthread.php?t=58065 I went through the latest vignette and not able to correlate w ...
deseq2 time course written 4 weeks ago by sum7320

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