Question: New package to identify differentially expressed genes from RNA-seq data
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gravatar for Naomi Altman
10.0 years ago by
Naomi Altman6.0k
Naomi Altman6.0k wrote:
I could not find this package on bioconductor.org. Thanks to rules about software downloads here, it will take a while for me to get R 2.10.0, and I would like to have a look at the documentation in the meantime. Where could I find it? Thanks, Naomi At 09:15 AM 10/14/2009, Likun Wang wrote: >Hi all, > We present a new R package DEGseq for identifying differentially >expressed genes from RNA-seq data.The input of DEGseq is uniquely mapped >reads from RNA-seq data with a gene annotation of the corresponding genome, >or gene (or transcript isoform) expression values provided by other >programs. The output of DEGseq includes a text file and an XHTML summary >page. The text file contains the expression values for the samples, a >P-value and two kinds of Q-values for each gene to denote its expression >difference between libraries. Two novel MA-plot based methods along with >some existing methods have been integrated into it. > > You may access it through the commands: > > source("http://bioconductor.org/biocLite.R") # R >= 2.10.0 > > biocLite("DEGseq") > > Comments, questions, etc, are all welcome. > Best regards >Likun > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
annotation degseq • 643 views
ADD COMMENTlink modified 10.0 years ago by Ulrike Goebel110 • written 10.0 years ago by Naomi Altman6.0k
Answer: New package to identify differentially expressed genes from RNA-seq data
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gravatar for Sean Davis
10.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Oct 14, 2009 at 4:18 PM, Naomi Altman <naomi@stat.psu.edu> wrote: > I could not find this package on bioconductor.org. Thanks to rules about > software downloads here, it will take a while for me to get R 2.10.0, and I > would like to have > a look at the documentation in the meantime. Where could I find it? > > http://bioconductor.org/packages/2.5/bioc/html/DEGseq.html > > At 09:15 AM 10/14/2009, Likun Wang wrote: > >> Hi all, >> We present a new R package DEGseq for identifying differentially >> expressed genes from RNA-seq data.The input of DEGseq is uniquely mapped >> reads from RNA-seq data with a gene annotation of the corresponding >> genome, >> or gene (or transcript isoform) expression values provided by other >> programs. The output of DEGseq includes a text file and an XHTML summary >> page. The text file contains the expression values for the samples, a >> P-value and two kinds of Q-values for each gene to denote its expression >> difference between libraries. Two novel MA-plot based methods along with >> some existing methods have been integrated into it. >> >> You may access it through the commands: >> > source("http://bioconductor.org/biocLite.R") # R >= 2.10.0 >> > biocLite("DEGseq") >> >> Comments, questions, etc, are all welcome. >> Best regards >> Likun >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 10.0 years ago by Sean Davis21k
Answer: New package to identify differentially expressed genes from RNA-seq data
0
gravatar for Likun Wang
10.0 years ago by
Likun Wang40
Likun Wang40 wrote:
You can find it at http://www.bioconductor.org/packages/2.5/bioc/html/DEGseq.html. Thanks for your attention, contact me anytime. 2009/10/15 Naomi Altman <naomi@stat.psu.edu> > I could not find this package on bioconductor.org. Thanks to rules about > software downloads here, it will take a while for me to get R 2.10.0, and I > would like to have > a look at the documentation in the meantime. Where could I find it? > > Thanks, > Naomi > > > At 09:15 AM 10/14/2009, Likun Wang wrote: > >> Hi all, >> We present a new R package DEGseq for identifying differentially >> expressed genes from RNA-seq data.The input of DEGseq is uniquely mapped >> reads from RNA-seq data with a gene annotation of the corresponding >> genome, >> or gene (or transcript isoform) expression values provided by other >> programs. The output of DEGseq includes a text file and an XHTML summary >> page. The text file contains the expression values for the samples, a >> P-value and two kinds of Q-values for each gene to denote its expression >> difference between libraries. Two novel MA-plot based methods along with >> some existing methods have been integrated into it. >> >> You may access it through the commands: >> > source("http://bioconductor.org/biocLite.R") # R >= 2.10.0 >> > biocLite("DEGseq") >> >> Comments, questions, etc, are all welcome. >> Best regards >> Likun >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > -- Likun Wang MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China Tel: +86-10-62794294 Fax: +86-10-62786911 Email: wang.likun@gmail.com [[alternative HTML version deleted]]
ADD COMMENTlink written 10.0 years ago by Likun Wang40
Answer: New package to identify differentially expressed genes from RNA-seq data
0
gravatar for Ulrike Goebel
10.0 years ago by
Ulrike Goebel110
Ulrike Goebel110 wrote:
Hi Likun, Likun Wang wrote: > Dear Ulrike, > > Are there invalid values in your gene expression file? That was it ! Some very high expression values had ","s introduces by Excel to separate the powers of thousand. After removing the commas, it works fine. Seems to be a nice package ! Best, Ulrike > Look at the following example. All the values should be numeric. > > > file1 <- "./test.txt" > > rt1 <- read.table(file1, header=FALSE,sep="\t") > > head(rt1,n=4) > V1 V2 V3 > 1 SGN-U573325 6.17 STRING1 > 2 SGN-U591447 0.77 <na> > 3 SGN-U592038 6.27 OK > 4 SGN-U573325 6.17 619.72 > > rt1[,2] > [1] 6.17 0.77 6.27 6.17 > > rt1[,3] > [1] STRING1 <na> OK 619.72 > Levels: 619.72 OK STRING1 > > mode(rt1[,2]) > [1] "numeric" > > mode(rt1[,3]) > [1] "numeric" # We do not want this > > mode(as(rt1[,2], "matrix")) > [1] "numeric" > > mode(as(rt1[,3], "matrix")) > [1] "character" # We want this > > Please contact me anytime if this problem is not fixed. > Thanks. > Best regards. > --------- > Likun > > 2009/10/15 Ulrike Goebel <ugoebel at="" mpiz-koeln.mpg.de=""> <mailto:ugoebel at="" mpiz-koeln.mpg.de="">> > > Dear Likun, > > I am not sure whether the following is a problem of your package, > or my input .. > > I wanted to compare two samples with a single replicate each, > using DEGseq(method="MARS"). > > The input file simply looks like this: > SGN-U573325 6.17 619.72 > SGN-U591447 0.77 101.16 > SGN-U592038 6.27 37.8 > ... > (The fields are tab-separated) > > >DEGexp(geneExpFile1=my_infile,expCol1=2, > geneExpFile2=my_infile,expCol2=3, > groupLabel1="condition1",groupLabel2="condition2", > method="MARS", > sep="\t", > header=FALSE > ) > Please wait... > Error in sum(exp_values) : invalid 'type' (character) of argument > > I traced this back by calling the routine in debug mode: > > debug: rt1 <- read.table(geneExpFile1, header = header, sep = sep) > Browse[2]>head(rt1,n=2) > V1 V2 V3 > 1 SGN-U573325 6.17 619.72 > 2 SGN-U591447 0.77 101.16 > Browse[2]> mode(rt1[,expCol1[i]]) > [1] "numeric" > > Browse[2]> > debug: exp_values <- as(rt1[expCol1[i]], "matrix") > Browse[2]> mode(exp_values) > [1] "character" > > I am not sure whether you have a reason to extract the columns > using "rt1[expCol1[i]]" rather > than "rt1[,expCol1[i]]" ? The latter *is* numeric ... > > Best regards > > Ulrike > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-08-01 r49053) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] DEGseq_0.99.0 samr_1.26 impute_1.18.1 qvalue_1.19.1 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > > > > > Likun Wang wrote: > > You can find it at > http://www.bioconductor.org/packages/2.5/bioc/html/DEGseq.html. > Thanks for your attention, contact me anytime. > > 2009/10/15 Naomi Altman <naomi at="" stat.psu.edu=""> <mailto:naomi at="" stat.psu.edu="">> > > > > I could not find this package on bioconductor.org > <http: bioconductor.org=""/>. Thanks to rules about > software downloads here, it will take a while for me to > get R 2.10.0, and I > would like to have > a look at the documentation in the meantime. Where could > I find it? > > Thanks, > Naomi > > > At 09:15 AM 10/14/2009, Likun Wang wrote: > > > > Hi all, > We present a new R package DEGseq for identifying > differentially > expressed genes from RNA-seq data.The input of DEGseq > is uniquely mapped > reads from RNA-seq data with a gene annotation of the > corresponding > genome, > or gene (or transcript isoform) expression values > provided by other > programs. The output of DEGseq includes a text file > and an XHTML summary > page. The text file contains the expression values for > the samples, a > P-value and two kinds of Q-values for each gene to > denote its expression > difference between libraries. Two novel MA-plot based > methods along with > some existing methods have been integrated into it. > > You may access it through the commands: > > source("http://bioconductor.org/biocLite.R") # R > >= 2.10.0 > > biocLite("DEGseq") > > Comments, questions, etc, are all welcome. > Best regards > Likun > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > > Naomi S. Altman > 814-865-3791 (voice) > Associate Professor > Dept. of Statistics > 814-863-7114 (fax) > Penn State University 814-865-1348 > (Statistics) > University Park, PA 16802-2111 > > > > > > > > > > > -- > Dr. Ulrike Goebel > Bioinformatics Support > Max-Planck Institute for Plant Breeding Research > Carl-von-Linne Weg 10 > 50829 Cologne > Germany > +49(0) 221 5062 121 > > > > > -- > Likun Wang > MOE Key Laboratory of Bioinformatics and Bioinformatics Div, > TNLIST / Department of Automation, Tsinghua University, > Beijing 100084, China > Tel: +86-10-62794294 > Fax: +86-10-62786911 > Email: wang.likun at gmail.com <mailto:wang.likun at="" gmail.com=""> -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121
ADD COMMENTlink written 10.0 years ago by Ulrike Goebel110
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