[BioC] from rat codelink to human locuslink
Weiwei Shi
helprhelp at gmail.com
Fri Nov 3 23:26:46 CET 2006
another question on this:
> getHomolog(id = "Rn.105679", from.type="unigene",
+ to.type="entrezgene",from.mart=rat, to.mart=human)
stack imbalance in .Call, 102 then 103
stack imbalance in <-, 100 then 101
stack imbalance in {, 98 then 99
stack imbalance in standardGeneric, 86 then 87
stack imbalance in class, 81 then 82
stack imbalance in <-, 79 then 80
stack imbalance in {, 77 then 78
stack imbalance in <-, 71 then 72
stack imbalance in {, 69 then 70
NULL
but I checked our database output:
Rn.105679
its corresponding human locuslink id = 54838,
I am really confused now at which is correct.
On 11/3/06, Weiwei Shi <helprhelp at gmail.com> wrote:
> Hi, Steffen:
>
> It seems that it works b/c my internal method (using Oracle + Python)
> gives me the same number of identified unigene ids but :
> > system.time(t0 <- getHomolog(id = ratUnigene, from.type="unigene",
> + to.type="entrezgene",from.mart=rat, to.mart=human))
> stack imbalance in .Call, 119 then 120
> stack imbalance in <-, 117 then 118
> stack imbalance in {, 115 then 116
> stack imbalance in standardGeneric, 103 then 104
> stack imbalance in class, 98 then 99
> stack imbalance in <-, 96 then 97
> stack imbalance in {, 94 then 95
> stack imbalance in <-, 88 then 89
> stack imbalance in {, 86 then 87
> [1] 11.284 15.534 32.705 0.000 0.000
> > dim(t0)
> [1] 4285 2
>
> so, what are those stack imbalance..?
>
> This time it really is fast. Thanks.
>
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
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