Entering edit mode
mariangela bonizzoni
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20
@mariangela-bonizzoni-5217
Last seen 10.4 years ago
Hi, I am trying to use DEseq to assess differential expression between
two
conditions "DE" and "un". I have 7 sets of comparisons. All my RNA-seq
libraries do NOT have biological replicates.
conds <- c("C.14.car.un", "C.14.car.DE", "C.14.mid.un" ,
"C.14.mid.DE",
"C.14.sal.un", "C.14.sal.DE", "C.01.car.un" , "C.01.car.DE",
"C.01.mid.un",
"C.01.mid.DE",
"C.04.car.un" , "C.04.car.DE", "C.04.mid.un", "C.04.mid.DE")
when i set:
cds.C.01.car <- cds[ , c("C.01.car.un", "C.01.car.DE") ]
cds.C.01.car <- estimateSizeFactors( cds.C.01.car )
cds.C.01.car <- estimateDispersions( cds.C.01.car, method="blind",
sharingMode="fit-only" )
res.C.01.car <- nbinomTest( cds.C.01.car, "C.01.car.un",
"C.01.car.DE" )
the program works fine, the same for conds C.14.car and C.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:
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 same error message for the other reaming conds. I tried changing
the
sharingMode to either "gene-est-only" and "maximum", but still got the
error message:
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
any advice is welcomed, thanks
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