Entering edit mode
Laurent Gautier
★
2.3k
@laurent-gautier-29
Last seen 10.3 years ago
On Wed, Oct 30, 2002 at 04:15:52PM -0500, Paul Boutros wrote:
> Hi again,
>
> > > > > The error message I get is:
> > > > > Error in rep(data, t1) : invalid number of copies in "rep"
> > > > >
> > > >
> > > > Try 'traceback()' just after the error message is fired. It
may give
> > > > us a hint about where this happened.
> > >
> > > I get:
> > > 3: rep(data, t1)
> > > 2: array(y.offset, (k - 1))
> > > 1: normalize.qspline(data2)
> > >
> > > Does this help at all?
>
> > It does. I had a hard time with the 'k' thing (and no answer from
the
> > corresponding author about my questions/remarks/suggestions). I
suspect
> > that for some reason you do not have the check added. Does the
code
> > for the function look like follows ?
> > -------------------
> > if (y.offset <= min.offset) {
> > y.offset <- min.offset;
> > k <- round(py.inds[1]/min.offset)
> > }
> >
> > ## here is the part I suspect missing ##
> > if (k < 1) {
> > warning("qspline cannot be performed (insufficient number of
> arrays)")
> > return(x)
> > }
> > ## ---- ##
> >
> > y.offset <- c(0, array(y.offset, (k-1)))
> > y.order <- order(target)
> > -------------------
>
> This is exactly how my code looks -- the check on array number is
not
> present.
> However, I should note that I am doing this analysis with three
arrays.
> The code I use looks like this:
>
> > data1 <- read.table("c:\\docume~1\\paul\\dev\\testvals.txt");
> > data2 <- data.matrix(data1);
> > data2;
> qry1.S635 qry1.S532 qry2.S635 qry2.S532 qry3.S635 qry3.S532
> H3001A10 613.0 602.5 483.0 633.0 61.0 75.0
> H3001A12 1208.5 1019.0 1209.0 1187.0 91.0 153.5
> H3001B01 337.0 353.0 619.0 529.5 132.5 153.5
> H3001C02 495.0 497.5 64.5 117.5 10.5 59.0
> H3001C03 199.5 152.5 301.0 222.0 63.5 95.5
> H3001C04 1855.5 1447.0 1969.0 1721.0 286.0 349.0
> H3001C07 4765.5 3643.0 4889.0 4401.5 1064.0 1148.0
> H3001C09 720.5 894.5 347.0 602.0 188.0 326.5
> H3001C11 630.0 536.0 814.5 899.5 20.0 48.5
> > c <- normalize.qspline(data2);
> Error in rep(data, t1) : invalid number of copies in "rep"
> > c <- normalize.qspline(data1);
> Error in rep(data, t1) : invalid number of copies in "rep"
>
> I tried adding the code you indicated as missing into the affy.R
file.
> I now get:
>
> qry1.S635 qry1.S532 qry2.S635 qry2.S532 qry3.S635 qry3.S532
> H3001A10 613.0 602.5 483.0 633.0 61.0 75.0
> H3001A12 1208.5 1019.0 1209.0 1187.0 91.0 153.5
> H3001B01 337.0 353.0 619.0 529.5 132.5 153.5
> H3001C02 495.0 497.5 64.5 117.5 10.5 59.0
> H3001C03 199.5 152.5 301.0 222.0 63.5 95.5
> H3001C04 1855.5 1447.0 1969.0 1721.0 286.0 349.0
> H3001C07 4765.5 3643.0 4889.0 4401.5 1064.0 1148.0
> H3001C09 720.5 894.5 347.0 602.0 188.0 326.5
> H3001C11 630.0 536.0 814.5 899.5 20.0 48.5
>
> Warning message:
> qspline cannot be performed (insufficient number of arrays) in:
> normalize.qspline(data2)
>
> This indicates to me that my input data is in an inappropriate
format
> somehow?
No. The format seems to be appropriate.
> Any ideas where I go from here?
>
I do. As mentioned earlier the variable 'k' is estimated in the code
through an iterative procedure (which has the annoying property to
give a value that do not make sense in some cases).
I contacted the corresponding author about that but get no answer.
I inserted the error message "insufficient blahblablah" since I
mainly observed that when applied with to a small number of arrays.
One way to get something done, waiting for the day I will have time to
go in details into that, would be to set a default value for k when
the
iterative things do not behave nicely.
Try to replace what you inserted with :
## ----------- ##
if (k < 1) {
warning("'k' things did not work. Set to default value")
k <- 5
}
## ---- ##
Hopin' it helps,
Laurent
