search for: tdt

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "G...

I am involved in a study where, as in most of life, men demonstrate themselves to be recalcitrant. So while we have many probands and most of their mothers we only have about 50% of the trios being complete. I have been running tdt and trio.types. It appears as if it is ignoring the duos. Sometimes a duo can be informative. For instance Father ..missing Mother 1/2 Proband 1/1 This duo shows that for allele 2, this was clearly a case where 2 was untransmitted. Yet I do not think this family counts toward the output that is ge...

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above would do 5...

Does anyone know if the sib TDT has been implemented in R 1. Spielman, R.S., and Ewens, W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 62, 450-458 -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

This ought to work: resultdt <- lapply(PGWide[, 240:389], function(x, ...) try(tdt(x, ...))) You can then check the class of each component to see which one failed. Andy From: Farrel Buchinsky > > "Berton Gunter" <gunter.berton at gene.com> wrote in message > news:008601c67097$de1b46e0$5bc4fea...

...igure the NIC through /etc/network/interfaces. Any attempt to use the NIC (eth2), such as a ping command, results in the following errors: root@gateway1:~# [ 98.816957] e1000: eth2: e1000_clean_tx_irq: Detected Tx Unit Hang [ 98.816963] Tx Queue <0> [ 98.816965] TDH <3> [ 98.816967] TDT <3> [ 98.816969] next_to_use <3> [ 98.816971] next_to_clean <0> [ 98.816973] buffer_info[next_to_clean] [ 98.816975] time_stamp <ffff398a> [ 98.816977] next_to_watch <0> [ 98.816979] jiffies <ffff3b88> [ 98.816981] next_to_watch.status <0> [ 100.816231] e10...

Hello, my server has massive problems with my NIC. I got: "Detected Tx Unit Hang". At the moment I use 2.6.31 from Jeremy, does anyone know if it''s fixed in 2.6.32 or newer tree? Regards, Stefan Kuhne _______________________________________________ Xen-devel mailing list Xen-devel@lists.xensource.com http://lists.xensource.com/xen-devel

Last Friday, Gregory Chaitin (http://www.umcs.maine.edu/~chaitin/lm.html) mentioned that there can be no proof that a given code is the shortest for a problem, even within a language. Still, the script below, a replacement of the "TDT", one of the most frequently used tests in genetics (http://mustat.rockefeller.edu under "downloads") may get close. It contains a few additional bytes for clarity, as in (2^1) for 2, but, otherwise, I don't think one could make this much shorter, especially the part that doe...

.../00002000 igb 0000:04:00.1: [ 0] Receiver Error (First) This spams to the console continuously until hard booting. - Supermicro X9DRD-iF/LF, Dual Xeon E5-2630, 2x I350, 2x 82575EB igb 0000:82:00.0: Detected Tx Unit Hang Tx Queue <1> TDH <43> TDT <50> next_to_use <50> next_to_clean <43> buffer_info[next_to_clean] time_stamp <12e6bc0b6> next_to_watch <ffff880006aa7440> jiffies <12e6bc8dc> desc.status <1c8210> This spams to...

...ut may not be used read.HapMap.data: local variable ?base? assigned but may not be used read.HapMap.data: local variable ?build? assigned but may not be used read.HapMap.data: local variable ?finish? assigned but may not be used read.HapMap.data: local variable ?strand? assigned but may not be used tdt.snp: local variable ?nc.snps? assigned but may not be used tdt.snp: local variable ?nr.snps? assigned but may not be used --------------------- which is more like expected check warnings. Care to comment? Hin-Tak Leung

...quot; "Data$Height.9" "Data$Height.10" "Data$Height.12""Data$Height.20"...but rather just to use the sapply function. However with some functions the sapply will not work and it is necessary to supply each variable name to a function (see thread at Repeating tdt function on thousands of variables) This is such a core capability. I would like to see it in the R-Wiki but could not find it there. -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

hello I'm having 2 problems with rsync... one is consequence of the other 1) I'm running an rsyncd one a server... then I run rync (client) as root on another server even being root, it doesn't read files/dirs with chmod 000 for example and gives error on them 2) when these error happens, it happens "IO error encountered" and it skip the "--delete" (I tried

.../00002000 igb 0000:04:00.1: [ 0] Receiver Error (First) This spams to the console continuously until hard booting. - Supermicro X9DRD-iF/LF, Dual Xeon E5-2630, 2x I350, 2x 82575EB igb 0000:82:00.0: Detected Tx Unit Hang Tx Queue <1> TDH <43> TDT <50> next_to_use <50> next_to_clean <43> buffer_info[next_to_clean] time_stamp <12e6bc0b6> next_to_watch <ffff880006aa7440> jiffies <12e6bc8dc> desc.status <1c8210> This spams to...

...Error (First) > > This spams to the console continuously until hard booting. > > - Supermicro X9DRD-iF/LF, Dual Xeon E5-2630, 2x I350, 2x 82575EB > > igb 0000:82:00.0: Detected Tx Unit Hang > Tx Queue <1> > TDH <43> > TDT <50> > next_to_use <50> > next_to_clean <43> > buffer_info[next_to_clean] > time_stamp <12e6bc0b6> next_to_watch <ffff880006aa7440> > jiffies <12e6bc8dc> > desc.status...

...the host. > > .. > [ 5959.338214] vfio-pci 0000:04:10.0: AMD-Vi: Event logged [IO_PAGE_FAULT domain=0x0037 address=0x7b657064 flags=0x0000] > [ 5963.353429] ixgbe 0000:03:00.0 enp3s0: Detected Tx Unit Hang > Tx Queue <0> > TDH, TDT <93>, <9d> > next_to_use <9d> > next_to_clean <93> > tx_buffer_info[next_to_clean] > time_stamp <10019e800> > jiffies &l...

...the host. > > .. > [ 5959.338214] vfio-pci 0000:04:10.0: AMD-Vi: Event logged [IO_PAGE_FAULT domain=0x0037 address=0x7b657064 flags=0x0000] > [ 5963.353429] ixgbe 0000:03:00.0 enp3s0: Detected Tx Unit Hang > Tx Queue <0> > TDH, TDT <93>, <9d> > next_to_use <9d> > next_to_clean <93> > tx_buffer_info[next_to_clean] > time_stamp <10019e800> > jiffies &l...

...t;> This spams to the console continuously until hard booting. >> >> - Supermicro X9DRD-iF/LF, Dual Xeon E5-2630, 2x I350, 2x 82575EB >> >> igb 0000:82:00.0: Detected Tx Unit Hang >> Tx Queue <1> >> TDH <43> >> TDT <50> >> next_to_use <50> >> next_to_clean <43> >> buffer_info[next_to_clean] >> time_stamp <12e6bc0b6> next_to_watch <ffff880006aa7440> >> jiffies <12e6bc8dc> >&gt...

...Error (First) > > This spams to the console continuously until hard booting. > > - Supermicro X9DRD-iF/LF, Dual Xeon E5-2630, 2x I350, 2x 82575EB > > igb 0000:82:00.0: Detected Tx Unit Hang > Tx Queue <1> > TDH <43> > TDT <50> > next_to_use <50> > next_to_clean <43> > buffer_info[next_to_clean] > time_stamp <12e6bc0b6> next_to_watch <ffff880006aa7440> > jiffies <12e6bc8dc> > desc.status...

...(I would've expected at least one sequential > computation, or non-standard design, but apparently there are none, or > I missed it). > David Clayton has a couple of little functions on his website, one for sequential analysis IIRC. I have some on my website for genetic association (TDT and case-control) and linkage (variance components) analysis. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd,...