[BioC] Qspline (again)

[Laurent Gautier]

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