[BioC] from rat codelink to human locuslink

[Durinck, Steffen (NIH/NCI) [F]]

Hi WeiWei,

I never encountered these stack imbalance messages and am wondering if they are produced by the system.time function which you wrapped around getHomolog.  There is no .Call function directly in the biomaRt code so it looks like this message is either coming from RMySQL or RCurl or system.time().
Do you also get these messages when running getHomolog directly without system.time?

best,
Steffen


-----Original Message-----
From: Weiwei Shi [mailto:helprhelp at gmail.com]
Sent: Fri 11/3/2006 5:03 PM
To: Durinck, Steffen (NIH/NCI) [F]
Cc: Diego Diez; bioconductor
Subject: Re: Re: [BioC] from rat codelink to human locuslink
 
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.