A permanent error in running your software

[beginner984]

Hi

After reading RCC and annotation file I get this error

> ## QC plots 
  > girafe( ggobj = autoplot( demoData , "lane-bindingDensity" ) )
Error:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "lane-fov" ) )
Error:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData, "housekeep-geom" ) ) 
Error:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "ercc-linearity" ) )
Error:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (375)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "ercc-lod" ) )
Error:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 2nd layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`, `outlier.data_id`, `outlier.tooltip`, `outlier.onclick`,
`outlier.hover_css`, `outlier.selected_css`, `outlier.tooltip_fill`, and `outlier.hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "boxplot-feature" , index = featureNames(demoData)[3] , elt = "exprs" ) )
Error in `stat_boxplot()`:
  ! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
  ! Aesthetics must be either length 1 or the same as the data (1)
x Fix the following mappings: `width`
Run `rlang::last_error()` to see where the error occurred.
> demoData <- normalize( demoData , type="nSolver", fromELT = "exprs" , toELT = "exprs_norm" )
Error in normalize(demoData, type = "nSolver", fromELT = "exprs", toELT = "exprs_norm") : 
  unused arguments (type = "nSolver", fromELT = "exprs", toELT = "exprs_norm")
> autoplot( demoData , "heatmap-genes" , elt = "exprs_norm" )
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': 'elt' not present in assayData(object)
> 
> demoData
NanoStringRccSet (storageMode: lockedEnvironment)
assayData: 784 features, 75 samples 
element names: exprs 
protocolData
sampleNames: _01_04.RCC _01_05.RCC ...
(75 total)
varLabels: FileVersion SoftwareVersion ... Sample ID (18 total)
varMetadata: labelDescription
phenoData
sampleNames: _01_04.RCC _01_05.RCC ...
(75 total)
varLabels: Group
varMetadata: labelDescription
featureData
featureNames: Endogenous_CCNO_NM_021147.4 Endogenous_MYC_NM_002467.3 ... Housekeeping_ERCC3_NM_000122.1 (784
                                                                                                         total)
fvarLabels: CodeClass GeneName ... BarcodeComments (10 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: NS_IO_360_v1.0 
signature: none
> 

Thanks for any help

[maddygriz]

Hi @beginner984 ,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email geomxsupport@nanostring.com with your issue.

Thanks, Maddy

[beginner984]

Sorry, shall I remove any sample gets TRUE in any fields of QC?

Like the first sample here

> tail(protocolData(demoData)[["QCFlags"]], 2)
                                Imaging Binding Linearity   LoD Housekeeping
20221.RCC   FALSE   FALSE     FALSE FALSE         TRUE
20222.RCC   FALSE   FALSE     FALSE FALSE        FALSE

Thanks for any intuition

[maddygriz]

Hi @beginner984 ,

Thank you for reaching out. Our customer support team will be able to help you with this. We have recently consolidated all the support emails into one. Please email support@nanostring.com with your issue.

Thanks, Maddy

[anke-king]

did you ever end up solving this problem? I get the same

[MaryGoAround]

I remember only I got the raw read matrix from the software and the rest I done out of software in R