[BioC] marrayPlot

Fri, 24 May 2002 02:18:05 +0200

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Hi,

I've just started using "R" with the bioconductor-packages. I'm now
trying to analyse our cDNA-array data.
Using the function "read.Spot" I've managed to import my data from a tab
separated file. After this, I've used the normalization function
"maNormMain(mbatch=TOR493, f.loc=list(maNormLoess(x="maA", y="maM",
z=NULL, w=NULL, subset=TRUE, span=0.4)), f.scale=NULL,
a.loc=maCompNormEq(), a.scale=maCompNormEq(), echo=FALSE)".

So far everything seems to be fine, but when I try to visualize my
results with "maDiagnPlots1(mraw=TOR493, title=NULL, save=FALSE)",
I get an error message "Error in rep(NA, maNspots(L)) : invalid number
of copies in "rep"". I don't understand this error message. What could
be wrong?

I'd appreciate if someone who has more experience than me could give me
any suggestions.

Regards,

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<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DSV =
style=3D'font-size:10.0pt;
font-family:Arial;mso-ansi-language:SV'>Hi,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DSV =
style=3D'font-size:10.0pt;
font-family:Arial;mso-ansi-language:SV'><o:p>&nbsp;</o:p></span></font></=
p>

I&#8217;ve just started using =
&#8221;R&#8221;
with the bioconductor-packages. I&#8217;m =
now trying
to analyse our cDNA-array
data.<o:p></o:p>

Using the function &#8220;read.Spot&#8221;
I&#8217;ve managed to import my data from a tab separated file. After =
this,
I&#8217;ve used the normalization function &#8220;maNormMain(mbatch=3DTOR493, f.loc=3Dlist(maNormLoess(x=3D&quot;maA&quot;,
y=3D&quot;maM&quot;, z=3DNULL, w=3DNULL, subset=3DTRUE, span=3D0.4)), =
f.scale=3DNULL,
a.loc=3DmaCompNormEq(), a.scale=3DmaCompNormEq(),
echo=3DFALSE)&#8221;.<o:p></o:p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>So far everything seems to be fine, but when I try to
visualize my results with &#8220;<span =
class=3DGramE>maDiagnPlots1(</span><span
class=3DSpellE>mraw</span>=3DTOR493, title=3DNULL, =
save=3DFALSE)&#8221;,<o:p></o:p></span></font></p>

I get an error message &#8220;Error in rep(NA,
maNspots(L)) : invalid number of copies in
&quot;rep&quot;&#8221;. I don&#8217;t understand this error message. =
What could
be wrong?<o:p></o:p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I&#8217;d appreciate if someone who has more =
experience than
me could give me any suggestions.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Regards,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

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