[BioC] gcrma background correction-saving output

Fri Dec 8 18:56:21 CET 2006

Hi Sucheta,

'exprs()' pulls out ALL of the probe-level values, even for MM probes and 
the gridding probes around the edges. If you want only the PM values, use 
'pm()'.

Cheers,
jenny

At 10:49 AM 12/8/2006, Sucheta Tripathy wrote:
>Thanks a lot Anbarasu!!
>
>It does work. Just wanted to make sure if any values change in this
>conversion process? My output look little srange though.
>
>Anyway, thanks a lot.
>
>Sucheta
>
>On Fri, December 8, 2006 3:55 am, Lourdusamy A Anbarasu wrote:
> > Hi,
> >
> >
> > You may need to use eSet object instead of 'AffyBatch'. So, use
> > exprs(tmp1).
> >
> > write.table(exprs(tmp1), file="out.txt", row.names=FALSE,
> > col.names=FALSE, sep="\t")
> >
> > Hope, this helps!
> > Anbarasu
> >
> >
> > On 12/7/06, Sucheta Tripathy <sutripa at vbi.vt.edu> wrote:
> >
> >>
> >> Dear List,
> >>
> >>
> >> Thanks to all who responded to my earlier question. While I can get
> >> going with reading multiple CEL files at a time for background
> >> correction, I would like to save the outputs of each CEL file as a
> >> separate text file. While I tried something like this to have the
> >> outputs as separate columns in one file:
> >>
> >> library(affy) library(gcrma) affinfo=compute.affinities("soybean") myDat
> >> <-ReadAffy()
> >> sessionInfo()
> >> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
> >> write.table(tmp1, file="out.txt", row.names=FALSE, col.names=FALSE,
> >> sep="\t")
> >>
> >> I get the following error
> >>
> >>
> >> Error:
> >> -------
> >> Error in as.data.frame.default(x[[i]], optional = TRUE) :
> >> cannot coerce class "AffyBatch" into a data.frame
> >>
> >> I hope somebody can help me with this.
> >>
> >>
> >> many thanks
> >>
> >> Sucheta
> >>
> >>
> >> On Wed, December 6, 2006 11:57 pm, Kasper Daniel Hansen wrote:
> >>
> >>> Most likely this is a bug coming from the fact that a matrix with 1
> >>> row (or column) usually gets silently changed to a vector. I am just
> >>> guessing based on the fact that it only seems to happen with 1 chip.
> >>> You
> >>> are only doing background adjusting which should work ok with only one
> >>>  chip - a full GCRMA with multichip summarization would not make a
> >>> whole lot of sense with 1 chip.
> >>>
> >>> Kasper
> >>>
> >>>
> >>>
> >>> On Dec 5, 2006, at 10:05 PM, Sucheta Tripathy wrote:
> >>>
> >>>
> >>>
> >>>> Hi Jean, List,
> >>>>
> >>>>
> >>>>
> >>>> Finally I managed to make the script
> >>>>
> >>>>
> >>>>
> >>>> library(affy) library(gcrma) affinfo=compute.affinities("soybean")
> >> myDat
> >>>> <-ReadAffy()
> >>>> sessionInfo()
> >>>> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo)
> >>>>
> >>>>
> >>>> run in my machine. The only thing I have noticed was it works with
> >>>> 2
> >>>> chips read simultaneously by ReadAffy(). For instance if I have only
> >>>>
> >> one
> >>>> CEL
> >>>> file instead of 2 CEL files in the working directory then I end up
> >> having
> >>>> the same error that I used to get before. Is there a reason for
> >>>> that?
> >>>>
> >>>> Error Message:
> >>>> --------------
> >>>>
> >>>>
> >>>>
> >>>> Adjusting for optical effect.Done.
> >>>> Computing affinities.Done.
> >>>> Error in model.frame(formula, rownames, variables, varnames, extras,
> >>>>  extranames,  : variable lengths differ (found for 'x') Execution
> >>>> halted -----
> >>>>
> >>>>
> >>>>
> >>>> my session info: ---------------- R version 2.4.0 (2006-10-03)
> >>>> i686-pc-linux-gnu
> >>>>
> >>>> locale:
> >>>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=e
> >>>> n_ US;LC_MESS
> >>>> AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M
> >>>> EA
> >>>> SUREMENT=e
> >>>> n_US;LC_IDENTIFICATION=C
> >>>>
> >>>> attached base packages: [1] "splines"   "tools"     "methods"
> >>>> "stats"
> >>>> "graphics"
> >>>> "grDevices"
> >>>> [7] "utils"     "datasets"  "base"
> >>>>
> >>>>
> >>>>
> >>>> other attached packages: soybeanprobe   soybeancdf        gcrma
> >>>> matchprobes affy       affyio "1.14.0"     "1.12.0"      "2.7.0"
> >>>> "1.6.0"
> >>>> "1.12.1"      "1.0.0"
> >>>> Biobase
> >>>> "1.12.2"
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> Thanks
> >>>>
> >>>>
> >>>>
> >>>> Sucheta
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Sucheta Tripathy, Ph.D.
> >>>> Virginia Bioinformatics Institute Phase-I
> >>>> Washington street.
> >>>> Virginia Tech.
> >>>> Blacksburg,VA 24061-0447
> >>>> phone:(540)231-8138
> >>>> Fax:  (540) 231-2606
> >>>>
> >>>>
> >>>>
> >>>> web page: http://staff.vbi.vt.edu/sutripa blog    :
> >>>> http://genomics-array.blogspot.com/
> >>>> quick ref: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/
> >>>> R_BioCondManual.html
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Bioconductor mailing list
> >>>> Bioconductor at stat.math.ethz.ch
> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>> Search the archives: http://news.gmane.org/
> >>>> gmane.science.biology.informatics.conductor
> >>>
> >>
> >>
> >> --
> >> Sucheta Tripathy, Ph.D.
> >> Virginia Bioinformatics Institute Phase-I
> >> Washington street.
> >> Virginia Tech.
> >> Blacksburg,VA 24061-0447
> >> phone:(540)231-8138
> >> Fax:  (540) 231-2606
> >>
> >>
> >> web page: http://staff.vbi.vt.edu/sutripa blog    :
> >> http://genomics-array.blogspot.com/
> >> quick ref:
> >> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> >
> >
> > --
> > Lourdusamy A Anbarasu
> > Dipartimento Medicina Sperimentale e Sanita Pubblica
> > Via Scalzino 3
> > 62032 Camerino (MC)
> >
> >
>
>
>--
>Sucheta Tripathy, Ph.D.
>Virginia Bioinformatics Institute Phase-I
>Washington street.
>Virginia Tech.
>Blacksburg,VA 24061-0447
>phone:(540)231-8138
>Fax:  (540) 231-2606
>
>web page: http://staff.vbi.vt.edu/sutripa
>blog    : http://genomics-array.blogspot.com/
>quick ref:
>http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html
>
>_______________________________________________
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>http://news.gmane.org/gmane.science.biology.informatics.conductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu