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Question: ABarray process error for ABI Human Genome Survey V2 data set
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gravatar for judemtaylor
7 days ago by
judemtaylor0 wrote:

Dear Bioconductor community,

I have read historical posts with the same problem but no solution has been posted to date. The contact provided in the ABarray vignette is out of date.

I am using the ABarray to process an Applied Biosystems GSE dataset using the human genome survey microarray version 2 platform.

I have checked that there are no differences in the sample names entered in the Data File and Experiment Design files (there are no differences) and I have named the respective columns according to the conventions described in the vignette.

it returns the following error while doing the basic analysis on non-normalised data using the 'ABarray' function. I have given the script below with the error:

Reading data from GSE_raw_data.csv ......
    This may take several minutes....
Finished data reading.
The results will be in the folder: Result_stage/

Perform basic analysis for non-normalized data ...
[1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3"
Error in err(isConflict[!isNull]) :
  assayData element dimnames conflict: exprs, flags, snDetect
In addition: There were 13 warnings (use warnings() to see them)

> warnings()
Warning messages:
1: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
2: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
3: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
4: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
5: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
6: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
7: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
8: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
9: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
10: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
11: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
12: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used
13: In grep(controlType, data[, colProbeID], ignore.case = TRUE) :
  argument 'pattern' has length > 1 and only the first element will be used

> traceback()
9: stop("assayData element dimnames conflict: ", paste(names(conflicts),
       collapse = ", "))
8: err(isConflict[!isNull])
7: dimConflict(dimNames, okNames, 2)
6: .harmonizeDimnames(.Object)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("ExpressionSet", phenoData = pheno, exprs = rawSig, snDetect = sn,
       flags = flag)
1: ABarray("GSE_raw_data.csv", "GSEpDataminimal.csv",
       "stage", test = TRUE, impute = "avg")

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)    

other attached packages:
[1] ABarray_1.44.0

Any suggestions or potential solution?

Thanks a lot,

Jude

 

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