[BioC] gcrma background correction-saving output

[Sucheta Tripathy]

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