Question: Time course cDNA two color array analysis
0
gravatar for Marcelo Laia
12.7 years ago by
Marcelo Laia430
Brazil
Marcelo Laia430 wrote:
Hi, My works was about a bacterium development in their host. I have 4 times points, in this way: Cy5 Cy3 NA 12h after inoculation NA 24h " NA 3 days " NA 5 days " Cy5 - culture medium Cy3 - host I look around the timecourse, limma, maSigPro, GeneCycle and GeneNet. However, all of then looks for me incompatible with two-colors arrays. Could you suggest me a way/strategy for to do my analysis? I am interested in genes which change over time. Thank you -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526
timecourse limma masigpro • 408 views
ADD COMMENTlink modified 12.7 years ago • written 12.7 years ago by Marcelo Laia430
Answer: Time course cDNA two color array analysis
0
gravatar for Ana Conesa
12.7 years ago by
Ana Conesa140
Ana Conesa140 wrote:
Hi Marcelo, I am not aware of GeneCycle and GeneNet, but maSigPro, limma, and I think timecourse also will take 2 color data. I do understand why you thought it was not possible. maSigPro will give you genes with changing expression profiles over time. You can follow the single series example given in the user?s guide. Limma allows you to make contrasts between time points. The tutorial has also a section about time course analysis. Ana On Fri, 19 Jan 2007 19:10:12 -0200, Marcelo Laia wrote > Hi, > > My works was about a bacterium development in their host. I have 4 > times points, in this way: > > Cy5 Cy3 > NA 12h after inoculation > NA 24h " > NA 3 days " > NA 5 days " > > Cy5 - culture medium > Cy3 - host > > I look around the timecourse, limma, maSigPro, GeneCycle and GeneNet. > However, all of then looks for me incompatible with two-colors > arrays. Could you suggest me a way/strategy for to do my analysis? I > am interested in genes which change over time. > > Thank you > > -- > Marcelo Luiz de Laia > Ph.D Candidate > S?o Paulo State University (http://www.unesp.br/eng/) > School of Agricultural and Veterinary Sciences > Department of Technology > Via de Acesso Prof. Paulo Donato Castellane s/n > 14884-900 Jaboticabal - SP - Brazil > Phone: +55-016-3209-2675 > Cell: +55-016-97098526 > > _______________________________________________ > 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 -- IVIA (http://www.ivia.es) Open WebMail Project (http://openwebmail.org) Debian Project (http://www.debian.org)
ADD COMMENTlink written 12.7 years ago by Ana Conesa140
Answer: Time course cDNA two color array analysis
0
gravatar for Marcelo Laia
12.7 years ago by
Marcelo Laia430
Brazil
Marcelo Laia430 wrote:
Dear Ana, I try to use replicate spot and I get trouble in set up the index, the match and matchID.col parameters. I do this code: > MA.2 <- normalizeWithinArrays(RG,method="printtiploess") > IDs <- MA.2$genes$names # match vector > indeX <- paste("g", rep(c(1:32), 216), sep = "") # index vector > masigproResult <- maSigPro(masigproData, add.IDs = FALSE, + IDs = NULL, matchID.col = 1, trat.repl.spots = "average", index = indeX, + match = IDs, rs = 0, design, vars = "groups", min.obs = 3) When I run this code, I get this error: [1] "running design" [1] "running p.vector" [1] "fitting gene 100 out of 5173" (...) [1] "running T.fit" [1] "fitting gene 100 out of 282" [1] "fitting gene 200 out of 282" [1] "running get.siggenes" Error in prom[i, ] <- c : subscript out of bounds In addition: There were 26 warnings (use warnings() to see them) I read the help pages for average.rows, get.siggenes e maSigPro and try the examples, but I don't understand how make these ones. I did a analysis without consider replicates, and it looks very good! I would like to compare the two results and get a little bit more knowledge. Thank you -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526
ADD COMMENTlink written 12.7 years ago by Marcelo Laia430
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