R numeric variable, non null, non na but empty - r

Question

Hi eveyrone ##.
I got some problem with R that I can't fix: Currently i'm working with GEOquery package and I want to retrieve some informations in metadata of gse files.
More precisely I'm looking for the channel label (for exemple Cye3). Here's a sample of my code :
>library(GEOquery)
>gse<-getGEO("GSE2253",GSEMatrix=TRUE,destdir=".")
>gse<-gse[[1]]
>gse$label_ch1[1]
V2
Levels: According to Affymetrix protocol (biotin)`
And here's my problem
`> is.na(gse$label_ch1[1])
V2
FALSE
> is.null(gse$label_ch1[1])
[1] FALSE`
This GSE file is a text file and in the line corresponding to the label (!Sample_label_ch1) there is no value.So, here's what I'v done for my work:
`if(is.na(gse$label_ch1[1])){
color<-"Non specified"
} else {
label<-gse$label_ch1[1]
}`
So, if I got no informations for the channel I just say "non specified", else, I return the value. But I'v got error with this if/else statement in my script:
Error in if (file == "") file <- stdout() else if (is.character(file)) { :
the length of argument is null
Sorry if the error traduction is not exact, my R version is in French ^^.
I tried
if(as.character(gse$label_ch1[1])=="")
But it doesn't work either
If someone has an idea to help me ^^
Thanks in advance!
Script:
sample<-NULL
output<-NULL
gse<-NULL
color<-NULL
series_matrix<-dir(getwd(),pattern="*series_matrix.txt")
series_matrix<-unlist(strsplit(series_matrix,"_")[1])
for(i in 1:length(series_matrix)){
gse<-getGEO(series_matrix[i],GSEMatrix=TRUE,destdir=".")
gse<-gse[[1]]
if(length(gse$label_ch1[1])==0){
color<-"Non specified"
} else {
color<-gse$label_ch1[1]
}
print (color)
sample<-cbind(as.character(gse$title),as.character(gse$geo_accession))
outputsample<-paste(getwd(),"/sample.txt",sep="")
write.table(paste("txt",color,sep=""),output,
row.names=FALSE,col.names=FALSE,sep="\t",quote=FALSE)
write.table(sample,outputsample,
row.names=FALSE,col.names=FALSE,sep="\t",quote=FALSE,append=TRUE)
Feature_Num<-list(1:length(featureNames(gse)))
Gene_Symbol<-pData(featureData(gse)[,11])
Probe_Name<-pData(featureData(gse)[,1])
Control_Type<-pData(featureData(gse)[,3])
liste<-as.character(sampleNames(gse))
for(i in 1:lenght(liste)){
values<-cbind(Feature_Num,Gene_Symbol,Probe_name,Control_Type,exprs(gse)[,i])
colnames(values)<-c("Feature_Num","Gene_Symbol",
"Probe_Name","Control_Type","gMedianSignal")
write.table(values,paste(getwd(),"/Ech",liste[i],".txt",sep=""),
row.names=FALSE,quote=FALSE,sep="\t")
}
}
Don't hesitate if you want explication about lines in this script

Answer 1

Yes, in R you can create a zero-length object:
foo<-vector()
foo
logical(0)
Then change it:
foo<-NULL
foo
NULL
It's confusing at first, but if you ever took some abstract algebra, you may remember the difference between the "empty set" and a set whose only element is the "empty set."

Answer 2

Asking on other forum I finally get a solution for this non NULL/non NA problem:
the gse$label_ch1[1] is numeric of length 1
> length(gse$label_ch1[1])
[1] 1
but we can transform this variable in character:
> as.character(gse$label_ch1[1])
[1] ""
and with this line
> nchar(as.character(gse$label_ch1[1]))
[1] 0
we can see that I can see if the gse$label_ch1[1] value is really empty or not
Thank you all for your help!
Cheers