[Bioc-devel] GEOquery: missing ID causes GDS2eSet to crash

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Thu Sep 17 14:07:21 CEST 2015

Dear developers of the GEOquery package,

> gds <- getGEO("GDS3666")
> eset <- GDS2eSet(gds)

results in the following error:

Error in value[[3L]](cond) : row names contain missing values
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?

I found out that this is due to a single NA in the ID list and that this
could be easily fixed by excluding NA's:

> check.na <- is.na(gds at dataTable@table$ID_REF)
> has.na <- any(check.na)
> gpl <- NULL
> if(has.na) {
+   ind <- !check.na
+   gds at dataTable@table <- gds at dataTable@table[ind,]
+   gpl <- getGEO(Meta(gds)$platform, AnnotGPL=TRUE)
+   gpl at dataTable@table <- gpl at dataTable@table[ind,]
+ }
> eset <- GDS2eSet(gds, GPL=gpl)

I wonder whether you want to include something similar in the GDSeSet
function in order to avoid these issues with NA's.


Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de

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