Question: gcrma background correction-saving output
0
gravatar for Jenny Drnevich
12.8 years ago by
Jenny Drnevich2.2k
Jenny Drnevich2.2k wrote:
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_BioCondManua l.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.ht ml > >_______________________________________________ >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 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. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
cdf affy gcrma matchprobes affyio • 527 views
ADD COMMENTlink modified 8 months ago by Bioconductor Community ♦♦ 0 • written 12.8 years ago by Jenny Drnevich2.2k
Answer: gcrma background correction-saving output
0
gravatar for Sucheta Tripathy
12.8 years ago by
Sucheta Tripathy170 wrote:
Thanks Jenny, It solved my long term problem. I get the expected output!! Best Regards. Sucheta On Fri, December 8, 2006 12:56 pm, Jenny Drnevich wrote: > 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=affi >>>>>> nfo) >>>>>> >>>>>> >>>>>> 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_MONETA >>>>>> RY=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 >> >> >> _______________________________________________ >> 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 >> > > 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. > Urbana, IL 61801 > USA > > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > -- 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.htm l
ADD COMMENTlink written 12.8 years ago by Sucheta Tripathy170
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