[BioC] marrayPlot
A.J. Rossini
rossini@u.washington.edu
23 May 2002 08:24:12 -0700
Is HTML mail really understandable? Parse the following. You might
try turning it off, else someone else can help you.
>>>>> "niklas" == Niklas Nordquist <niklas.nordquist@genpat.uu.se> writes:
niklas> <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40">
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niklas> <p class=MsoNormal><font size=2 face=Arial><span lang=SV style='font-size:10.0pt;
niklas> font-family:Arial;mso-ansi-language:SV'>Hi,<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span lang=SV style='font-size:10.0pt;
niklas> font-family:Arial;mso-ansi-language:SV'><o:p> </o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>I’ve just started <span class=GramE>using ”</span>R”
niklas> with the <span class=SpellE>bioconductor</span>-packages. I’m now trying
niklas> to <span class=SpellE>analyse</span> our <span class=SpellE>cDNA</span>-array
niklas> data.<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>Using the function “<span class=SpellE>read.Spot</span>”
niklas> I’ve managed to import my data from a tab separated file. After this,
niklas> I’ve used the normalization function “<span class=SpellE><span
niklas> class=GramE>maNormMain</span></span><span class=GramE>(</span><span
niklas> class=SpellE>mbatch</span>=TOR493, <span class=SpellE>f.loc</span>=list(<span
niklas> class=SpellE>maNormLoess</span>(x="<span class=SpellE>maA</span>",
niklas> y="maM", z=NULL, w=NULL, subset=TRUE, span=0.4)), <span class=SpellE>f.scale</span>=NULL,
niklas> <span class=SpellE>a.loc</span>=<span class=SpellE>maCompNormEq</span>(), <span
niklas> class=SpellE>a.scale</span>=<span class=SpellE>maCompNormEq</span>(),
niklas> echo=FALSE)”.<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'><o:p> </o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>So far everything seems to be fine, but when I try to
niklas> visualize my results with “<span class=GramE>maDiagnPlots1(</span><span
niklas> class=SpellE>mraw</span>=TOR493, title=NULL, save=FALSE)”,<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>I get an error message “Error in <span class=GramE>rep(</span>NA,
niklas> <span class=SpellE>maNspots</span>(L)) : invalid number of copies in
niklas> "rep"”. I don’t understand this error message. What could
niklas> be wrong?<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'><o:p> </o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>I’d appreciate if someone who has more experience than
niklas> me could give me any suggestions.<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'><o:p> </o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'>Regards,<o:p></o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'><o:p> </o:p></span></font></p>
niklas> <p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
niklas> font-family:Arial'><o:p> </o:p></span></font></p>
niklas> </div>
niklas> </body>
niklas> </html>
--
A.J. Rossini Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics rossini@u.washington.edu
FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org
-------------- http://software.biostat.washington.edu/ ----------------
FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email
UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX
(my friday location is usually completely unpredictable.)