Sorry, I'll try to provide more detail about what I have done so far with
code and any relevant output results.
>library(qtl)
>sawfly.cross <- read.cross(format="csv",
file="~/Desktop/Sawfly_data/QTL/Sawfly_QTL.csv", na.strings="NA",
genotypes=c("A", "B"), alleles=c("A", "B"), estimate.map=F)
--Read the following data:
430 individuals
506 markers
19 phenotypes
--Cross type: bc
>print(sawfly.cross)
--This is an object of class "cross".
It is too complex to print, so we provide just this summary.
Backcross
No. individuals: 430
No. phenotypes: 19
Percent phenotyped: 99.8 99.8 99.3 99.1 99.1 99.1 99.1 99.1 99.5 99.8
99.8 99.5 98.8 99.8 99.8 99.8 99.8 98.4 99.5
No. chromosomes: 7
Autosomes: 1 2 3 4 5 6 7
Total markers: 506
No. markers: 103 89 75 74 65 51 49
Percent genotyped: 96.2
Genotypes (%): AA:49.7 AB:50.3
Backcross
No. individuals: 430
No. phenotypes: 19
Percent phenotyped: 99.8 99.8 99.3 99.1 99.1 99.1 99.1 99.1 99.5 99.8
99.8 99.5 98.8 99.8 99.8 99.8 99.8 98.4 99.5
No. chromosomes: 7
Autosomes: 1 2 3 4 5 6 7
Total markers: 506
No. markers: 103 89 75 74 65 51 49
Percent genotyped: 96.2
Genotypes (%): AA:49.7 AB:50.3
>sawfly.cross <- calc.genoprob(sawfly.cross, step=2.5, error.prob=0.1,
map.function="kosambi", stepwidth="fixed")
**I am using head size as a covariant.**
>head.covar <- pull.pheno(sawfly.cross, pheno.col=19)
>sawfly.cross.stepwise.peryellow <- scantwo(sawfly.cross, pheno.col=2,
model="normal", method="hk", addcovar=head.covar, use="all.obs",
clean.output=F, verbose=T, n.perm=1000, batchsize=100);
save.image("~/Desktop/Sawfly_data/QTL/SawflyQTL.RData")
--Warning messages:
1: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, :
Dropping 1 individuals with missing phenotypes.
2: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, :
Dropping 1 individuals with missing covariates.
> sawfly.cross.stepwise.peryellow.pen <- calc.penalties(alpha=0.05,
perms=sawfly.cross.stepwise.peryellow)
>> sawfly.cross.stepwise.peryellow.stepqtl <- stepwiseqtl(sawfly.cross,
pheno.col=2, method="hk", max.qtl=10,
penalties=sawfly.cross.stepwise.peryellow.pen , verbose=T,
keeplodprofile=T, covar=head.covar, scan.pairs=F, keeptrace=T)
--Error in covar[!hasmissing, , drop = FALSE] : incorrect number of
dimensions
**I corrected this with the next piece of code
>sawfly.cross.stepwise.peryellow.stepqtl <- stepwiseqtl(sawfly.cross,
pheno.col=2, method="hk", max.qtl=10,
penalties=sawfly.cross.stepwise.peryellow.pen , verbose=T,
keeplodprofile=T, covar=as.data.frame(sawfly.cross$pheno$Head.Area),
scan.pairs=F, keeptrace=T)
The stepwise than ran and I got to the point where I got the warning
message I posted
about:Warning message:
In lastout[[i]] - (max(lastout[[i]]) - dropresult[rn == qn[i], 3]) :
longer object length is not a multiple of shorter object length
I proceeded to examine the output
>sawfly.cross.stepwise.peryellow.stepqtl
QTL object containing genotype probabilities.
name chr pos n.gen
Q1 1@106.1 1 106.11 2
Q2 2@180.0 2 179.97 2
Q3 3@181.9 3 181.91 2
Q4 3@181.9 3 181.91 2
Q5 5@142.5 5 142.50 2
Formula: y ~ sawfly.cross$pheno$Head.Area + Q1 + Q2 + Q3 + Q4 + Q5 +
Q4:Q5
pLOD: 166.23
In my late night of googling, I did see that the warning can indicate that
dimensions of the arguments do not match, but I do not know how to
translate that to my data or output.
Thank you.
On Sat, May 23, 2015 at 3:36 AM, Uwe Ligges <lig...@statistik.tu-dortmund.de
> wrote:
>
>
> On 23.05.2015 01:07, Claire O'Quin wrote:
> > Hi There,
> >
> > I am running a stepwise QTL for a backcross and got the following warning
> > message:
> >
> > Warning message:
> > In lastout[[i]] - (max(lastout[[i]]) - dropresult[rn == qn[i], 3]) :
> > longer object length is not a multiple of shorter object length
>
> So dimensions of the arguments may not match?
> >
> > I can not discern what this means. When I created my plot, the QTL curve
> on
> > chromosome 3 is very odd (tried attaching it), so I suspect that the
> > warning is connected to that odd curve plot.
> >
> > I tried running the fitqtl just to see what would happen and got an error
> > (Error in solve.default(t(Z) %*% Z, t(Z) %*% X) : system is
> computationally
> > singular: reciprocal condition number = 1.49755e-24).
> >
> > Any thoughts about what is going on?
>
> No, without knoing what the arguments and the actual code was.
>
> Best,
> Uwe Ligges
>
> >
> > Thank you,
> > Claire
> >
> >
> >
> > -----------------------------------
> > Claire O'Quin, PhD
> > Postdoctoral Research Scholar
> > University of Kentucky
> > http://www.linnenlab.com/home.html
> >
> >
> >
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
--
-----------------------------------
Claire O'Quin, PhD
Postdoctoral Research Scholar
University of Kentucky
http://www.linnenlab.com/home.html
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