[BioC] error in dispersion estimate
mariangela bonizzoni
mbonizzoni at gmail.com
Thu Apr 12 17:24:20 CEST 2012
Hi
I am trying to use DESeq to test for differential expression between two
conditions "DE" and "un". I do NOT have biological replicates. I have 7
comparisons.
conds <- c("CTM.14.car.un", "CTM.14.car.DE", "CTM.14.mid.un" , "CTM.14.mid.DE",
"CTM.14.sal.un", "CTM.14.sal.DE", "CTM.01.car.un" , "CTM.01.car.DE",
"CTM.01.mid.un", "CTM.01.mid.DE",
"CTM.04.car.un" , "CTM.04.car.DE", "CTM.04.mid.un", "CTM.04.mid.DE")
When i set:
cds.CTM.01.car <- cds[ , c("CTM.01.car.un", "CTM.01.car.DE") ]
cds.CTM.01.car <- estimateSizeFactors( cds.CTM.01.car )
cds.CTM.01.car <- estimateDispersions( cds.CTM.01.car, method="blind",
sharingMode="fit-only" )
res.CTM.01.car <- nbinomTest( cds.CTM.01.car, "CTM.01.car.un", "CTM.01.car.DE"
)
it works fine, (the same for CTM.14.car, CTM.01.mid)
but when i set:
cds.CTM.04.car <- cds[ , c("CTM.04.car.un", "CTM.04.car.DE") ]
cds.CTM.04.car <- estimateSizeFactors( cds.CTM.04.car )
cds.CTM.04.car <- estimateDispersions( cds.CTM.04.car, method="blind",
sharingMode="fit-only" )
i get the error message (the same for CTM.04.car, CTM.04.mid, CTM.14.mid,
CTM.14.sal):
Error in parametricDispersionFit(means, disps) :
Parametric dispersion fit failed. Try a local fit and/or a pooled estimation.
(See '?estimateDispersions')
In addition: Warning message:
glm.fit: algorithm did not converge
The option pooled was not liked because i do not have replicates. Any solutions?
thanks
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