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marrayPlot

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Niklas Nordquist ▴ 20

@niklas-nordquist-30

Last seen 9.6 years ago

This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C202C9.3D1E4070 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit 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, ------=_NextPart_000_0001_01C202C9.3D1E4070 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <html xmlns:o="3D" urn:schemas-microsoft-com:office:office""="=" ""="" xmlns:w="3D" urn:schemas-microsoft-com:office:word""="=" ""="" xmlns="3D" <a="" href="<a href=" http:="" www.w3.org="" TR="" REC-html40"="" rel="nofollow">http://www.w3.org/TR/REC-html40" rel="nofollow">http://www.w3.org/TR/REC-html40""> <head> <meta http-equiv="3D" Content-Type""="" content="3D" text="" html;"="=" ""="" charset="3Dus-ascii" "=""> <meta name="3DProgId" content="3DWord.Document"> <meta name="3DGenerator" content="3D" Microsoft"="" word="" 10"=""> <meta name="3DOriginator" content="3D" Microsoft"="" word="" 10"=""> <link rel="3DFile-List" href="3D" cid:filelist.xml@01C202C9.3D0190B0""=""> <style> </style> </head> <body lang="3DEN-US" link="3Dblue" vlink="3Dpurple" =="" style="3D'tab-interval:.5in'">

Hi,<o:p></o:p>

<o:p> </o:p>

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

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=3DTOR493, f.loc=3Dlist(maNormLoess(x=3D"maA", y=3D"maM", z=3DNULL, w=3DNULL, subset=3DTRUE, span=3D0.4)), = f.scale=3DNULL, a.loc=3DmaCompNormEq(), a.scale=3DmaCompNormEq(), echo=3DFALSE)”.<o:p></o:p>

<o:p> </o:p>

So far everything seems to be fine, but when I try to visualize my results with “maDiagnPlots1(mraw=3DTOR493, title=3DNULL, = save=3DFALSE)”,<o:p></o:p>

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?<o:p></o:p>

<o:p> </o:p>

I’d appreciate if someone who has more = experience than me could give me any suggestions.<o:p></o:p>

<o:p> </o:p>

Regards,<o:p></o:p>

<o:p> </o:p>

</body> </html> ------=_NextPart_000_0001_01C202C9.3D1E4070--

Normalization Normalization • 1.1k views

ADD COMMENT • link updated 21.9 years ago by Sandrine Dudoit ▴ 170 • written 21.9 years ago by Niklas Nordquist ▴ 20

score 0 · Answer 1 · 2002-05-23

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="<a href=" http:="" www.w3.org="" TR="" REC-html40"="" rel="nofollow">http://www.w3.org/TR/REC-html40"> niklas> <head> niklas> <meta http-equiv="Content-Type" content="text/html; charset=us-ascii"> niklas> <meta name="ProgId" content="Word.Document"> niklas> <meta name="Generator" content="Microsoft Word 10"> niklas> <meta name="Originator" content="Microsoft Word 10"> niklas> <link rel="File-List" href="cid:filelist.xml@01C202C9.3D0190B0"> niklas> niklas> <style> niklas> niklas> </style> niklas> niklas> </head> niklas> <body lang="EN-US" link="blue" vlink="purple" style="tab- interval:.5in"> niklas>

niklas>

Hi,<o:p></o:p>

niklas>

<o:p> </o:p>

niklas>

I’ve just started using ”R” niklas> with the bioconductor-packages. I’m now trying niklas> to analyse our cDNA-array niklas> data.<o:p></o:p>

niklas>

Using the function “read.Spot” niklas> I’ve managed to import my data from a tab separated file. After this, niklas> I’ve used the normalization function “ class=GramE>maNormMain( class=SpellE>mbatch=TOR493, f.loc=list( class=SpellE>maNormLoess(x="maA", niklas> y="maM", z=NULL, w=NULL, subset=TRUE, span=0.4)), f.scale=NULL, niklas> a.loc=maCompNormEq(), class=SpellE>a.scale=maCompNormEq(), niklas> echo=FALSE)”.<o:p></o:p>

niklas>

<o:p> </o:p>

niklas>

So far everything seems to be fine, but when I try to niklas> visualize my results with “maDiagnPlots1( class=SpellE>mraw=TOR493, title=NULL, save=FALSE)”,<o:p></o:p>

niklas>

I get an error message “Error in rep(NA, niklas> maNspots(L)) : invalid number of copies in niklas> "rep"”. I don’t understand this error message. What could niklas> be wrong?<o:p></o:p>

niklas>

<o:p> </o:p>

niklas>

I’d appreciate if someone who has more experience than niklas> me could give me any suggestions.<o:p></o:p>

niklas>

<o:p> </o:p>

niklas>

Regards,<o:p></o:p>

niklas>

<o:p> </o:p>

niklas>

<o:p> </o:p>

niklas>

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.)

score 0 · Answer 2 · 2002-05-23

Hi Niklas, I've noticed some problems with maDiagnPlots1 in windows, but not the one you are referring to. I'll look into it. Best, Sandrine On Fri, 24 May 2002, Niklas Nordquist wrote: > 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, > > >