How to use erccdashboard with erccmix="Single" design
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adi.rotem • 0
@adirotem-19954
Last seen 15 months ago
Israel

Hello! I am trying to use erccdashboard with the option erccmix="Single", since I have only samples with mix1. I'm struggling to understand how to run "runDashboard" in this case. The Vignettes states that I just need to state erccmix="Single". When I run the code with erccmix="RatioPair", everything runs fine. But when I run the same data and inputs with erccmix="Single" I get an error when trying to run "exDat <- dynRangePlot(exDat)":

Error in data.frame(Feature = levels(dataFit$Feature), AveConc = AveConc,  : 
  arguments imply differing number of rows: 74, 73

An my data looks like this: enter image description here

and when I ran this code:

    exDat <- initDat(datType="count", isNorm=FALSE,
                 exTable=data,
                 filenameRoot="testRun",  erccmix="Single",sample1Name="MET",
                 sample2Name="CTL",
                 erccdilution=1/40,
                 spikeVol=1.3, # ul
                 totalRNAmass=1, # ug
                 choseFDR=0.1)
    exDat <- dynRangePlot(exDat)

The output looks like this:

    exDat <- dynRangePlot(exDat)

mRNA fraction estimate is assumed to be equal to 1
Number of ERCCs in Mix 1 dyn range:  85 

Number of ERCCs in Mix 2 dyn range:  85 
These ERCCs were not included in the signal-abundance plot,
because not enough non-zero replicate measurements of these
 controls were obtained for both samples:

ERCC-00017 ERCC-00024 ERCC-00147 ERCC-00061 ERCC-00075
ERCC-00081 ERCC-00083 ERCC-00117 ERCC-00137 ERCC-00138
ERCC-00168
Error in data.frame(Feature = levels(dataFit$Feature), AveConc = AveConc,  : 
  arguments imply differing number of rows: 74, 73
RNASeqData erccdashboard • 509 views
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