User: arabella23

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arabella230
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Posts by arabella23

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Answer: A: Factoring analysis and better design
... A colleague of mine suggested to add another column called nested.patient then the design will be nested.patient+group, is this correct?Can you explain why not design= ~group+nested.patient?  sampleName patient condition time group nested.patient A16_6_12_12 A16 ...
written 23 months ago by arabella230
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Answer: A: Factoring analysis and better design
... Another question: Am I correct that log2Foldchange >1 means that the output given by DESeq2 is a fold change of 2.    Is there also a way of getting a ratio of fold change in DESeq wherein after doing the contrast of a group you like, I can also compare the ratio of two fold changes among each ...
written 23 months ago by arabella230
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Answer: A: Factoring analysis and better design
... I think I figured out, I will just make a nested design at the end. Thanks. ...
written 23 months ago by arabella230
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Answer: A: Factoring analysis and better design
... Hi Mike, I checked all and they are factors. Yes they also do have equal number of patients in each condition which is 5 patients, 3 time points. This is what I did: condition=factor(colData$condition) time=factor(colData$time) patient=factor(colData$patient) > class (time) [1] "factor" > ...
written 23 months ago by arabella230
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Factoring analysis and better design
... Hi Michael and other DESeq2 users, My dilemma is setting the best analysis for this design.  I have been trying the following code: dds <-DESeqDataSetFromMatrix(countData=counttable, colData=colData, design= ~group) dds <- DESeq (dds) This works but I want to take account the patient so m ...
deseq deseq2 written 23 months ago by arabella230

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