Question: Gene symbols and IDs in R and problem with clinical details
0
gravatar for marco
4.1 years ago by
marco10
Italy
marco10 wrote:

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

R • 1.9k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by marco10

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

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by marco10

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

ADD REPLYlink written 4.1 years ago by Sean Davis25k
0
gravatar for Sean Davis
4.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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))

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Sean Davis25k
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