search for: cy5

...thing into "all.Rout" file? If the "for" loop is removed, t.test output can be written into "all.out". Thanks in advance. Minghua Yao ...... zz <- file("all.Rout", open="wt") sink(zz) for(i in 1:n) { Cy3<-X[,2*i-1]; Cy5<-X[,2*i]; t.test(Cy3, Cy5) } sink() close(zz) ......

Hi, I have some microarray data, cy5 and cy3 values are in log2. Is there a way to check they have undergone lowess normalization ? Thanks Stanley [[alternative HTML version deleted]]

Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to normalize using spike in controls. My controls are annotated as CTL-1 to x and i would like to do etiher a normalization by block pe...

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Hello sir: As to the "variance stabilization" method which is applied in the "vsn"package under R environment,here's a question about the ratio of the 2 channels: After applying vsn,we can get new_cy5 and new_cy3 intensity according to the original cy5 and cy3 intensity respectively. And the new_cy5 new_cy3 are similar with ln(intensity). But how can I calculate the ratio=cy5/cy3 ? If the new_cy5 and new_cy3 is log2(intensity),the ratio equals to 2^(log2cy5-log2cy3),but as to vsn,how to get t...

...9;RG' looks like a pre-2.4.0 S4 object: please recreate it > objects() [1] "RG" > names(RG) [1] "R" "G" "Rb" "Gb" "printer" "genes" "targets" > RG$targets FileName Cy3 Cy5 c1 a1koc1.spot Pool C57BL/6 c2 a1koc2.spot Pool C57BL/6 c3 a1koc3.spot Pool C57BL/6 c4 a1koc4.spot Pool C57BL/6 c5 a1koc5.spot Pool C57BL/6 c6 a1koc6.spot Pool C57BL/6 c7 a1koc7.spot Pool C57BL/6 c8 a1koc8.spot Pool C57BL/6 k1 a1kok1.spot Pool ApoAI-/- k2 a1kok2.spot Pool ApoAI-/- k3 a1kok3...

...t only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward way to do this, or a valuable function, but I've been using my own methods and going around in circles. So far I've normalized within and between arrays, then returned the RG values using RG<-RG.MA, then I...

...National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov <mailto:roger.vallejo@ars.usda.gov> **************************************** > targets SlideNumber FileName Cy3 Cy5 ml12med 12 ml12med.spot CD4 CD8 ml13med 13 ml13med.spot CD8 CD4 ml14med 14 ml14med.spot DN CD8 ml15med 15 ml15med.spot CD8 DN ml16med 16 ml16med.spot CD4 DN ml17med 17 ml17med.spot DN CD4 > design <- modelMatrix(targets, ref="CD4") Found unique target names: CD4 CD8 DN...

Dear all, I need some help on matrix design and B statistics by using limma package. I want to compare gene expression in 2 groups of cDNA samples. The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice (#5,#6,#7,#8). The target file is FileName Cy3 Cy5 mice1.spot Control_#5 Treat_#1 mice2.spot Treat_#1 Control_#5 mice3.spot Control_#6 Treat_#2 mice4.spot Treat_#3 Control_#7 mice5.spot Control_#8 Treat_#4 The first slide (mice1.spot) and the second slide(mice2.spot) are dye-swap. There is no common reference. There are 3 r...

...ect the reliability of the final result? Can I continue to the next step? Thanks! Dejian Zhao ++++++++++++++++++ Program Starts +++++++++++++++++++++ > library(limma) > library(statmod) #duplicateCorrelation requires this package. > targets<-readTargets() > targets Cy3 Cy5 FileName Date 1 PLAIN PLATEAU Locust 186.gpr 2006-5-31 2 PLAIN PLATEAU Locust 187.gpr 2006-5-31 3 PLAIN PLATEAU Locust 188.gpr 2006-5-31 4 PLAIN PLATEAU Locust 189.gpr 2006-5-31 5 PLAIN PLATEAU Locust 190.gpr 2006-5-31 6 PLAIN PLATEAU Locust 191.gpr 2006-5-31 7 plain...

Hi I have two lots of numbers which I would like to histogram using the hist() function. For comparative reasons, I want them to be on the same scale, which I can use the xlim and ylim options to achieve. However, having them on the same scale is meaningless unless they have the same "breaks". Consulting the documentation, there are 4 ways of defining the number of breaks, only one