**10**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

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

10Try adding "ifnotfound=NA" to the mget() call. The new approach is to use select(). See the AnnotationDBI vignette for details.

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