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michael watson IAH-C
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3.4k
@michael-watson-iah-c-378
Last seen 10.1 years ago
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