edgeR: design matrix setup
On 05/23/2012 07:24 AM, rmje wrote:
I have a data frame like this:
T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h
C0h C0.25h C0.5h C1h C2h C3h C6h C12h C24h C48h
NM_001001130 68 95 56 43 66 62 68 90 63 89 65
85 58 49 81 49 76 73 48 77
NM_001001152 79 129 52 50 24 45 130 154 112 147 56
85 67 33 52 31 93 77 65 109
...
...
...
It has about 29000 rows and 20 columns (incl col.name).
How would you set this up in edgeR if you want to compare the 10 first with
the 10 last?
Please ask questions about Bioconductor packages on the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ There have been recent time-course questions on the mailing list, so it's good to browse recents posts. Remember to include sessionInfo(). Have you looked at the extensive vignette for this package http://bioconductor.org/packages/2.10/bioc/html/edgeR.html and limma, and taken a stab at answering your own question? It helps to see where you're coming from...; for this particular question and if you're statistically naive it might help to have a conversation with someone local who is a little versed in statistics. Martin
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