User: marburg2107

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Posts by marburg2107

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Comment: C: Deseq2: 3 factors design
... Thanks for your help! I just have 6 treatments as co2(400ppm),co2(480ppm), co2(400ppm)+drought(125mm), co2(480ppm)+drought(125mm),co2(400ppm)+drought(125mm)+warm(yes),co2(400ppm)+drought(125mm)+warm(no). As you said, we should have 8 treatments. BUT they did not do other treatments. I want to kn ...
written 4 weeks ago by marburg21070
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Comment: C: Deseq2: 3 factors design
... 1. DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~ co2 + warm+ drought+co2:warm+co2:drought) (no problem) 2. DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~ co2 + warm+ drought+co2:warm+co2:drought+co2:warm:drought)(the model matrix is not full ra ...
written 4 weeks ago by marburg21070
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Comment: C: Deseq2: 3 factors design
... The design of the experiment looks like: sample co2 warm drought a11 400ppm yes 125mm a12 400ppm yes 125mm a13 400ppm yes 125mm a14 400ppm yes 125mm a21 400ppm yes 125mm a22 400ppm yes 125mm a23 400ppm yes 125mm a24 400ppm yes 125mm a31 400ppm yes 125mm a32 400ppm yes 125mm a33 400ppm yes 125mm a34 ...
written 4 weeks ago by marburg21070
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Comment: C: Deseq2: 3 factors design
... Total 72 samples, 6 treatment,12 replicates. 6 treatments were: co2-400ppm, co2-400ppm+drought, co2-400ppm+drought+warm, co2-600ppm, co2-600ppm+drought,co2-600ppm+drought+warm ...
written 4 weeks ago by marburg21070
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Answer: A: Deseq2: 3 factors design
... countData = read.table ("C:/Users/bei/Desktop/deseq2/kegg.txt", sep= "\t", row.names = 1, head = TRUE) colData = read.table ("C:/Users/bei/Desktop/deseq2/151617-new2.txt", sep= "\t", row.names = 1, header = TRUE) colData[['co2']] = factor(colData[['co2']], levels = c('TRUE', 'FALSE')) colData[[' ...
written 4 weeks ago by marburg21070
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Answer: A: Deseq2: 3 factors design
... DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~co2+warm+drought+co2:warm+co2:drought+warm:drought+co2:warm:drought) --------------Error in checkFullRank(modelMatrix) My R version is 3.4.2 (2017-09-28), Deseq2 version is 1.18.1 ...
written 4 weeks ago by marburg21070
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Deseq2: 3 factors design
... It's really complicated for me to handle three-factors with DESeq2, though many of the posts on Biostars.I think the developer should make it more clear to users. Three factors are temperature(A, B); water content (C, D); co2 concentration (E, F). I want to know the following effects: (1)temperatu ...
deseq2 design three factors written 4 weeks ago by marburg21070

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