Question: InSilicoMerging error when using merge
0
gravatar for andreas.pittroff
2.6 years ago by
andreas.pittroff0 wrote:

Hello all,

I am currently trying to merge two expressionsets using the merge-function of InSilicoMerging.

Here is the code I was using (error translates to "error in data frame [...] arguments imply differing number of rows: 181, 107":

 mergeset = merge(esets)
Fehler in data.frame(<S4 object of class "ExpressionSet">, <S4 object of class "ExpressionSet">,  :
  Argumente implizieren unterschiedliche Anzahl Zeilen: 181, 107

 

Traceback:
> traceback()
10: stop(gettextf("arguments imply differing number of rows: %s",
        paste(unique(nrows), collapse = ", ")), domain = NA)
9: data.frame(<S4 object of class "ExpressionSet">, <S4 object of class "ExpressionSet">,
       check.names = TRUE, stringsAsFactors = TRUE)
8: eval(expr, envir, enclos)
7: eval(as.call(c(expression(data.frame), x, check.names = !optional,
       stringsAsFactors = stringsAsFactors)))
6: as.data.frame.list(x)
5: as.data.frame(x)
4: merge(as.data.frame(x), as.data.frame(y), ...)
3: merge.default(esets)
2: merge(esets)
1: merge(esets)

 

The two expressionsets look like this:

> eset1b
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 181 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM1213669 GSM1213670 ... GSM1213849 (181 total)
  varLabels: title geo_accession ... data_row_count (35 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16
    total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL570
> eset3b
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 107 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM254625 GSM254626 ... GSM254731 (107 total)
  varLabels: title geo_accession ... data_row_count (35 total)
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total)
  fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16
    total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL96

 

Merge did definitely run before on my system using this line, when I did load the expressionsets using InsilicoDB. InSilicoDB is currently not working however, so I am using GEOquery to import the datasets I downloaded with InSilicoDB before (maybe there is a problem here?)

 

Regards

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by andreas.pittroff0

The function merge() from insilicodb is obscured by basic R merge, try to run inSilicoMerging::merge(esets, method="NONE")

ADD REPLYlink written 9 months ago by Adam_M0
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