Does negative corfit$consensus cause issues while fitting a model in limma
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@mohammedtoufiq91-17679
Last seen 17 days ago
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Hi,

I am analyzing NanoString transcriptome data. The design of my study is as follows:

Each subject has 1 measurement only (cell line), however 2 subjects have two measurements (cell lines). I have 21 samples in total that corresponds to 19 subjects and there are 2 types of cell lines. Basically, trying to identify differentially exp. genes between two cell lines. I was able to run lmFit, Does negative corfit$consensus cause issues while fitting a model in limma results?

corfit <- duplicateCorrelation(data,design,block=Sample_metadata$`Subject ID`)
corfit$consensus 
[1] -0.5054192

Thank you,

Toufiq ```

limma R design model.matrix • 141 views
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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

Yes, it does cause an issue. Since the correlation is negative, you should remove blocking from the linear model. Estimating correlations from just two repeated subjects is pretty hard anyway.

I would also suggest trouble-shooting your data, because my guess is that one of the four samples belonging to the two subjects with repeat cell lines is an outlier.

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Hi Gordon Smyth thank you very much for the inputs and suggestions.

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