[BioC] Errors when running maPlot function from marrayPlots

[michael watson (IAH-C)]

Hi 

I am running Windows XP, R version 1.7.1 and Bioconductor 1.2, installed about 2 weeks ago from the website.  I am getting some errors with maPlot from the marrayPlots package.

A bit about the data that I am having problems with - it is not a great data set, and often the background corrected intensity in one or more of the chanels is negative.  In fact with one particular dataset, in the Cy5 channel, the MAJORITY of spots are negative.  

Now, when I run the command:

>maPlot(data[,2], x="maA", y="maM", z="maPrintTip")

I get the errors:

Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize,  : 
        NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 50 or more warnings (use warnings() to see the first 50)

The types of warning I get are at the end of the e-mail.  

You will note that this data set is not a good one, and I think it contains a MAJORITY of NA values rather than actual values.  However, I get the same errors if I change all the negative intensities to a value of 1, so it can't be the abundance of NA's that causes the error.....

What I do know is that if I do:

>maPlot(data[,2], x="maA", y="maM", z=NULL)

I don't get any errors, and if I do it on a different data set with less negatives, that works too (with no errors).

So I guess it is something to do with the print tip method - perhaps Lowess needs a wide range of values to work on and due to the nature of the data set that doesn't exist...??  Or perhaps the default range is greater than the number of valid data points???

As an aside, I opened up the same data using the limma module and using the plotPrintTipLoess method, I got NO errors, though I did get some pretty useless Lowess lines - but those were due to the nature of the data, not to any error in limma.  And there are values, both positive and negative, in every print tip group, so it is not the absence of data in a particular print tip group....So just wondering why my data won't work in marrayPlots.....?  Any ideas?

(incidentally I did get an error in limma, but thats for my next mail)

Thanks in advance for any help :-D

Mick

> warnings()
Warning messages:
1: pseudoinverse used at 8.1624
2: neighborhood radius 0.7843
3: reciprocal condition number  0
4: There are other near singularities as well. 0.86751
5: pseudoinverse used at 8.1624
6: neighborhood radius 0.7843
7: reciprocal condition number  0
8: There are other near singularities as well. 0.86751
9: pseudoinverse used at 8.1624
10: neighborhood radius 0.7843
11: reciprocal condition number  0
12: There are other near singularities as well. 1.6073
13: pseudoinverse used at 8.1624
14: neighborhood radius 0.7843
15: reciprocal condition number  0
16: There are other near singularities as well. 1.6073