On Feb 13, 2010, at 3:18 AM, Sahil Seth wrote:
Hi,
I have been trying to find a solution to this issue, but have not
been able
to so !
I am trying to use sapply on the function getSYMBOL,
The annotate package is from BioConductor.
an extract from the list is:
test.goP[13:14]
$`GO:0000050`
IEA IEA IEA IEA TAS TAS TAS
IEA
"5270753" "5720725" "1690128" "4850681" "110433" "2640544" "4900370"
"1430280"
IEA NAS TAS IEA
"6110044" "1170615" "6590546" "1690632"
$`GO:0000052`
[1] NA
goG=sapply(test.goP,getSYMBOL,data="hgu95av2")
I was a bit surprised to see a data= argument to sapply. That didn't
seem typical but perhaps I am not aware of all the tricks available.
error: "Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs "
In this the 14th element has missing values, thus getSYMBOL raises
issues.
The way this is being displayed makes me think you are processing a
list with named elements. You should use str to determine what
test.goP really is. Then you will have a better idea what functions
would be appropriate. you may want to compose a function to go with
the sapply loop that omots the NA's:
?na.omit
You should also post the results of dput or dump on the test objects
you are working with. That way the list readers can also get access to
that information.
GetSYMBOL has to be given a char array, so a simple solution is
infact to
delete the missing elements from the list.
I have been trying to find a solution for it, but in vain:
tried: completecases(goP), na.omit(goP) and several other things.
Any suggestions please ?
In addition to the above suggestions ... post on the correct list?
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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