negative correlation?
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 2.9 years ago
United States
I am running limma 2.8 on a technical replicate dye-swap design. Here is my design matrix: (Intercept) as.factor(targets$time)24h as.factor(targets$time)4h as.factor(targets$time)8h 1 -1 0 0 0 2 1 0 0 0 3 -1 0 0 0 4 1 0 0 0 5 -1 0 1 0 6 1 0 1 0 7 -1 0 1 0 8 1 0 1 0 9 -1 0 0 1 10 1 0 0 1 11 -1 0 0 1 12 1 0 0 1 13 -1 1 0 0 14 1 1 0 0 15 -1 1 0 0 16 1 1 0 0 corfit <- duplicateCorrelation(MA, design=designTimeR,ndups = 1, block = targets$biorep) targets$biorep [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 > corfit$con [1] -0.3414428 Why am I getting a negative correlation between bio reps? Is this expected due to the dye swap? --Naomi
limma limma • 869 views
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 2.9 years ago
United States
Oops again. The limma manual explains this. Too quick on the send button as usual. --Naomi At 01:24 PM 6/29/2011, Naomi Altman wrote: >I am running limma 2.8 on a technical replicate dye-swap >design. Here is my design matrix: > >(Intercept) as.factor(targets$time)24h as.factor(targets$time)4h >as.factor(targets$time)8h >1 -1 0 0 > 0 >2 1 0 0 > 0 >3 -1 0 0 > 0 >4 1 0 0 > 0 >5 -1 0 1 > 0 >6 1 0 1 > 0 >7 -1 0 1 > 0 >8 1 0 1 > 0 >9 -1 0 0 > 1 >10 1 0 0 > 1 >11 -1 0 0 > 1 >12 1 0 0 > 1 >13 -1 1 0 > 0 >14 1 1 0 > 0 >15 -1 1 0 > 0 >16 1 1 0 > 0 > > >corfit <- duplicateCorrelation(MA, design=designTimeR,ndups = 1, >block = targets$biorep) > >targets$biorep > [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 > > > > corfit$con >[1] -0.3414428 > >Why am I getting a negative correlation between bio reps? Is this >expected due to the dye swap? > >--Naomi > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
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