search for: yeast

...n 2.9.0 Under development (unstable) (2009-02-21 r47969) here is the output: > organism="human" > species <- switch(organism, human <- "Hs", fly <- "Dm", mouse <- "Mm", rat <- "Rn", yeast <- "Sc" ) species <- switch(organism, + human <- "Hs", + fly <- "Dm", + mouse <- "Mm", + rat <- "Rn", + yeast <- "Sc" + ) > species [1] "Hs" > organism="yeast" > species...

...uggest or help (or have time) in optimizing this code to make it run faster. My programming skills are not high enough to do it. Thanks, Monica #### code follows: #### x a data frame with over 30000 points with coord in UTM, xeast, xnorth #### y a data frame with over 4000 points with UTM coord (yeast, ynorth) and ##### classification ### calculating Euclidian distance dist <- function(xeast, xnorth, yeast, ynorth) { ((xeast-yeast)^2 + (xnorth-ynorth)^2)^0.5 } ### doing the merge by location with minimum distance dist.merge <- function(x, y, xeast, xnorth, yeast, ynorth){ tmp <- t(a...

Dear R-expert, For histogram function, can we get the table of bin and frequency like in excel, together with the histogram? Therefore, we can check the number of data included. Thank you so much for your attention and help. ____________________________________________________________________________________ [[elided Yahoo spam]]

Hello to everyone, I am trying to compute a mean and show it to the screen and then save to later be used as a boxplot.I have used the following code: dat<-read.table(file="C:\\Documents and Settings\\Owner\\My Documents\\Yeast\\Yeast.txt",header=T,row.names=1) file.show(file="C:\\Documents and Settings\\Owner\\My Documents\\Yeast\\Yeast.txt") x<-dat[2,23:46] y=mean(x,trim=0,na.rm=T) save(y,file="ydata") Am I computing the mean correctly and how to I show the value of the mean to the screen?...

Hello everyone, I am trying to subset a matrix with the following code: dat<-read.table(file="C:\\Documents and Settings\\Owner\\My Documents\\Yeast\\Yeast.txt",header=T,row.names=1) file.show(file="C:\\Documents and Settings\\Owner\\My Documents\\Yeast\\Yeast.txt") Z.matrix<-as.matrix(dat) Y<-array(dat,dim(,[46:63]) but I keep getting the error message: error in dim element 1 is empty I am trying to subset the columns 46-6...

...variable rather than a string? For example: xx$"YAL002" works, but this doesn't: gene <- "YAL002" xx$gene neither do xx$parse(gene) xx$eval(gene) xx$eval(parse(gene)) or a variety of other constructions I have tried. Background: I have a table of information about yeast genes, and I also have a list of yeast genes and their GO terms (xx) from the YEAST package that I downloaded. I want to go through all the genes in my table and look up their GO terms in the list from the YEAST package. They might not contain exactly the same genes (ideally they should, but I'...

...ntributed (I've just started using it)...I have a few questions that I am having some trouble finding the answer to: I am using RPgSQL to grab some data from a postgresql database (about 179 columns and a few thousand rows), and I want to do a lot of pairwise comparison of the rows...(this is yeast genomic microarray data for those who care) I get to the database: > db.connect(dbname="yeast") and grab the first two rows like this: > t<-sql.select(columns="*", from="gasch", limit=2) then create two lists a la: > a<-t[1,][4:length(t[1,])] >...

Hello, I have a y-axis label that reads: "S. schenckii yeast cells". The part that reads "S. schenckii" needs to be in italic style, the rest of the text is normal style. How can I specify the different font styles for each part of the y-axis label? Thank you, Judith

Just download Wbfs Manager 3.0 , trying to load it and it doesnt work , at first the icon wasnt right , add to change the permission details , now it looks like its trying to load but it isnt . Its the first program that im trying to load with wine so maybe im missing something or its because of the program ... http://wbfsmanager.codeplex.com/ If someone knows how to load it , some help would be

Hello I am sorry fuch such a stupid question. Suppose I have a table of data having a lot of NAs and I want to replace those NAs by the mean of the column before NA replacement. How is it possible to do that efficiently ? Thanks in advance, Julie -- Julie Bernauer Yeast Structural Genomics http://www.genomics.eu.org

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Dear cateGOry experts, hyperGTest documentation states that YEAST cannot be used as 'annotation' when evaluating gene ontology representation status for a given set of 'geneIds'. Because I am using a custom print I believe I need to create my own data package to use as the annotation file for 'annotation'. Can someone please describe how...

Dear R community Hope all of you are fine. I have a question regarding the an error message. Actually, I am trying to generate classification trees using "tree" package. It works well but for some datasets e.g., wine, yeast, boston housing etc. it gives an error message. Error in tree(V14 ~ ., data = training.data, method = c("recursive.partitioning"), : maximum depth reached The structure of getting output is given below: iris.tr = tree(Species ~., data=training.data, method=c("recursive.p...

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Dear R and Bioconductor Helpers, I am using a package called RankProd under Bioconductor to analysis my Y98 (yeast) microarray data. I had no problem following the example in the vignette but got stocked when I tried to analyze my own data. When I tried to run the following command, RP.out <- RP(rrf.sub, rrf.cl.sub, gene.names = y98.gnames, rand = 123) I got the following response: Rank Product analysi...

...hpages at latitude Rpacks]$ ls AnnotationDbi/inst/AnnDbPkg-templates/ AFFYHUEX.DB CHIMP.DB MALARIA.DB WORM.DB ANOPHELES.DB COELICOLOR.DB MOUSECHIP.DB XENOPUSCHIP.DB ARABIDOPSISCHIP.DB ECOLICHIP.DB MOUSE.DB XENOPUS.DB ARABIDOPSIS.DB ECOLI.DB ORGANISM.DB YEASTCHIP.DB BASEPKG.DB FLYCHIP.DB PFAM.DB YEAST.DB BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB CANINECHIP.DB HUMANCHIP.DB RATCHIP.DB ZEBRAFISH.DB CANINE.DB HUMAN.DB RAT.DB CH...

Thanks. Workarounds are interesting but... what's the point of the NOTE in the first place? H. On 2/4/24 09:07, Duncan Murdoch wrote: > On 04/02/2024 10:55 a.m., Izmirlian, Grant (NIH/NCI) [E] via R-devel > wrote: >> Well you can see that yeast is exactly weekday you have.? The way out >> is to just not name the result > > I think something happened to your explanation... > >> >> toto <- function(mode) >> { >> ???? ifelse(mode == 1, >> ???????? function(a,b) a*b, >> ???????? function(...

Well you can see that yeast is exactly weekday you have. The way out is to just not name the result toto <- function(mode) { ifelse(mode == 1, function(a,b) a*b, function(u, v, w) (u + v) / w) } ________________________________ From: Grant Izmirlian <izmirlidroid at gmail.com> Date: Sun, Feb 4...

...of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is platform and R version independant. The file that I'm reading contains the upstream regions of the yeast genome, with each upstream region labeled using a FASTA header, i.e.: FASTA header for gene 1 upstream region..... ..... .... FASTA header for gene 2 upstream.... .... The script I use - code below - opens the file, parses for a FASTA header, and then parses the head...

On 04/02/2024 10:55 a.m., Izmirlian, Grant (NIH/NCI) [E] via R-devel wrote: > Well you can see that yeast is exactly weekday you have. The way out is to just not name the result I think something happened to your explanation... > > toto <- function(mode) > { > ifelse(mode == 1, > function(a,b) a*b, > function(u, v, w) (u + v) / w) > } It's a bad i...