Help with design for 2 controls in infection time points with deseq2
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diya.sen • 0
@diyasen-16460
Last seen 4.4 years ago
Swedish University of Agricultural Scie…

Hey 

I have RNASeq results from infection time points, 24hr, 48hr and 72hr that I would like to compare to 2 controls, M (mycelia)

 and S (sporangia). See the metadata below. I am interested in pairwise comparisons for each infection time point and control i.e., M vs 24hr, M vs 48hr, M vs 72hr etc but I would also like to know if there is any difference for using M vs S as control. I think in the former I would do the following;

condition = c(rep("M",3), rep("S",3),rep("24hr",3),rep("48hr",3),rep("72hr",3))

dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)

Trouble is I don't know how to set up the latter, i.e., I think I wold need a 3rd column with control1, control2 and treatment. But I'm not sure. 

Please help!!!

 

  sample condition

P5467_101         M
P5467_102         M
P5467_103         M
P5467_104         S
P5467_105         S
P5467_106         S
P5467_107      24hr
P5467_108      24hr
P5467_109      24hr
P5467_110      48hr
P5467_111      48hr
P5467_112      48hr
P5467_113      72hr
P5467_114      72hr
P5467_115      72hr

deseq2 • 333 views
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Entering edit mode
@mikelove
Last seen 59 minutes ago
United States

Please take a look at the time course example in the workflow:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments

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