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Got Error in getFirehoseData function #9

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luoyuan1984 opened this issue Jan 4, 2019 · 1 comment
Open

Got Error in getFirehoseData function #9

luoyuan1984 opened this issue Jan 4, 2019 · 1 comment

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@luoyuan1984
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luoyuan1984 commented Jan 4, 2019

Hello, I am trying to run code below:

# Download GISTIC results
lastanalyzedate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",gistic2Date = lastanalyzedate)

# get GISTIC results
gistic.allbygene <- getData(gistic, type = "GISTIC", platform = "AllByGene")

I got an error like this:
Error in getData(gistic, type = "GISTIC", platform = "AllByGene") :
No data available for that type

I also tried to view gistic by view(gistic), but got another error:
Error in if (more || nchar(output) > 80) { :
missing value where TRUE/FALSE needed

I am using R:3.5.1 and RStudio:1.1.456 in Windows10 system.

Thank you.

@tiagochst
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It seems they updated the package.
Thanks for pointing it out.
The updated code is below.

library(RTCGAToolbox)
lastanalyzedate <- getFirehoseAnalyzeDates(1)
gistic <- getFirehoseData("GBM",GISTIC = TRUE, gistic2Date = lastanalyzedate)

# get GISTIC results
gistic.allbygene <- getData(gistic, type = "GISTIC", platform = "AllByGene")
gistic.thresholedbygene <- getData(gistic, type = "GISTIC", platform = "ThresholdedByGene")

Sorry for the late reply. I did not get notified.

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