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@dataTable@table$ID_REF)
> has.na <- any(check.na)
> gpl <- NULL
> if(has.na) {
+ ind <- !check.na
+ gds@dataTable@table <- gds@dataTable@table[ind,]
+ gpl <- getGEO(Meta(gds)$platform, AnnotGPL=TRUE)
+ gpl@dataTable@table <- gpl@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.
Best,
Ludwig
--
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.geistlin...@bio.ifi.lmu.de
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