Gene symbols and IDs in R and problem with clinical details

Question

[marco]

Hi everyone,

I'm trying to work with GSE48350 but, when i want take the ids and the symbol, R give me back an error:

p=row.names(mygcrma)
s = unlist(get(p, hgu133ahsentrezgSYMBOL))
Error in unlist(get(p, hgu133ahsentrezgSYMBOL)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "1007_s_at" not found
ID = unlist(mget(p, hgu133ahsentrezgENTREZID))
Error in unlist(mget(p, hgu133ahsentrezgENTREZID)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "1007_s_at" not found

Can you help me? :)

Edit,

I've another problem when i try to download the clinical details;

GSE48350_clindata=getGSEDataTables("GSE48350")
GSE48350_clindata
list()
length(GSE48350_clindata)
[1] 0

Thanks

[marco]

What is the new approach? :)

Edit:

I think that in your reply you mean hgu133plus2hsentrezgSYMBOL and not hgu133aplus2SYMBOL, but it still does not work.

> s = unlist(mget(p, hgu133plus2hsentrezgSYMBOL))
There were 20 warnings (use warnings() to see them)
Error in unlist(mget(probes, hgu133plus2hsentrezgSYMBOL)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "1007_s_at" not found
> ID = unlist(mget(p, hgu133plus2hsentrezgENTREZID))
Warning messages:
1: In (function ()  :
  hgu133plus2hsentrezgCHR is deprecated. Please use an appropriate TxDb object or package for this kind of data.
2: In (function ()  :
  hgu133plus2hsentrezgCHRLENGTHS is deprecated. Please use an appropriate TxDb object or package for this kind
  of data.
3: In (function ()  :
  hgu133plus2hsentrezgCHRLOC is deprecated. Please use an appropriate TxDb object or package for this kind of
  data.
4: In (function ()  :
  hgu133plus2hsentrezgCHRLOCEND is deprecated. Please use an appropriate TxDb object or package for this kind of
  data.
5: In (function ()  :
  hgu133plus2hsentrezgCHR is deprecated. Please use an appropriate TxDb object or package for this kind of data.
6: In (function ()  :
  hgu133plus2hsentrezgCHRLENGTHS is deprecated. Please use an appropriate TxDb object or package for this kind
  of data.
7: In (function ()  :
  hgu133plus2hsentrezgCHRLOC is deprecated. Please use an appropriate TxDb object or package for this kind of
  data.
8: In (function ()  :
  hgu133plus2hsentrezgCHRLOCEND is deprecated. Please use an appropriate TxDb object or package for this kind of
  data.
Error in unlist(mget(probes, hgu133plus2hsentrezgENTREZID)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "1007_s_at" not found

[Sean Davis]

Try adding ifnotfound=NA to the mget() call. The new approach is to use select(). See the AnnotationDBI vignette for details.

Answer 1

[Sean Davis]

Answering your second question first, GSE48350 has no GSE Data Tables, so the result you are getting is correct. The sample metadata are usually included with the ExpressionSet that is available via getGEO:

eset = getGEO("GSE48350")[[1]]
head(pData(eset))

As for the feature annotation, you are using an older approach, but to answer your question directly, I'm not sure where you got hgu133ahsentrezg, but the library you need is hgu133plus2 and this should work:

ID = unlist(mget(featureNames(eset),hgu133plus2SYMBOL))