On Sun, Mar 9, 2014 at 1:11 PM, Ming Yi <yi02@hotmail.com> wrote:

> Hi, Mike:
>
> Thx for your advice again and I did try what you suggested as below:
>
> > dds <- DESeqDataSetFromMatrix(countData = countD,colData = colD,design =
> ~Type + RasType + Type:RasType);
> > dds <- DESeq(dds);
> estimating size factors
> estimating dispersions
> gene-wise dispersion estimates
> mean-dispersion relationship
> final dispersion estimates
> fitting generalized linear model
> 105 rows did not converge in beta, labelled in mcols(object)$betaConv. Use
> larger maxit argument with nbinomWaldTest
> > show(resultsNames(dds));
> [1] "Intercept"                   "Type_Tumor_vs_Normal"
> [3] "RasType_RasP_vs_RasOnly"     "RasType_RasP1Hit_vs_RasOnly"
> [5] "RasType_RasPNot_vs_RasOnly"  "TypeTumor.RasTypeRasP"
> [7] "TypeTumor.RasTypeRasP1Hit"   "TypeTumor.RasTypeRasPNot"
>
> certainly we can use
> > res_RasP_vs_RasOnly <- results(dds,"RasType_RasP_vs_RasOnly")
> > res_RasP_vs_RasOnly <- results(dds,name="RasType_RasP_vs_RasOnly")
> > res_Tumor_vs_Normal<-results(dds,"Type_Tumor_vs_Normal")
> > res_Tumor_vs_Normal<-results(dds,name="Type_Tumor_vs_Normal")
>
> but I can not do the following with contrast as suggested in section 3.2:
> > res_Tumor_vs_Normal<-results(dds,contrast=c("Type","Tumor","Normal"))
> Error in results(dds, contrast = c("Type", "Tumor", "Normal")) :
>   unused argument (contrast = c("Type", "Tumor", "Normal"))
> >  res_RasP_vs_RasOnly <-
> results(dds,contrast=c("RasType","RasP","RasOnly"))
> Error in results(dds, contrast = c("RasType", "RasP", "RasOnly")) :
>   unused argument (contrast = c("RasType", "RasP", "RasOnly"))
>
> also I can not get contrast like Tumor.RasP_Tumor.RasPNot:
> > res_Tumor.RasP_Tumor.RasPNot<-results(dds,contrast=c(0,0,0,0,0,1,0,-1))
> Error in results(dds, contrast = c(0, 0, 0, 0, 0, 1, 0, -1)) :
>   unused argument (contrast = c(0, 0, 0, 0, 0, 1, 0, -1))
>
> it seems the interaction terms in the design (design = ~Type + RasType +
> Type:RasType) changed the behavior of results()?
>
>
Hi, Ming.

Be sure to include the output of sessionInfo() when you report errors.  The
information from that command tells us what version of R and OS you are
using and what packages and package versions you have loaded.

Sean

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