similar to: how to use writeFASTA in modality "append"

I realize function write FASTA expects a list with two items, respectively, description and sequence. However, just passing a list won't work (please, see code at the bottom of this message) I saw there is the helper function CharacterToFASTArecords(x) that presumably generates the right input data format. It would b very useful to get some example of CharacterToFASTArecords(x) usage. The

Has anybody solved this issue. [ http://rubyforge.org/pipermail/facebooker-talk/2008-April/000552.html ] ? NameError (undefined local variable or method `controller'' for #<LeaveController:0xb7144abc>): /app/controllers/application.rb:24:in `verify_authenticity_token''

Hi all, I'm having some trouble in understanding how to ste the Error() term in the aov() function when fitting a hierarchical ANOVA. I have data concerning the expression of 2 miRNAs in 3 different cell lines, with 2 different extraction methods. The data is organized as follows : Line Extraction Target Expression 1 BC54 miRNA RNU48 22.48 2 BC54 miRNA

Dear R-users, I'm using lattice package and function xyplot for the first time so you will excuse me for my inexperience. I'm facing quite a simple problem but I'm having troubles on how to solve it, I've read tons of old mails in the archives and looked at some slides from?Deepayan Sarkar but still can not get the point. This is the context. I've got data on 9 microRNAs, each

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

Hi there, I wonder if there is a way of efficiently generating a correlation matrix of two expression matrices. I want to correlate miRNA and mRNA expression and used the following code: ##dat.mi miRNA expression matrix, dat.m mRNA expression matrix nc <- nrow(dat.mi) cor.mat <- data.frame(rep(NA,nrow(dat.m))) pval.mat <- data.frame(rep(NA,nrow(dat.m))) for(i in 1:nc) { cr <- vector()

Hi all! While I am trying to read .cel files with oligo package: afbatch=read.celfiles(list.celfiles()) I get an error: Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository How can I overcome this? Thank you in advance

Hi , We've downloaded the CELTV0.11.1 source code from celt-codec.org . But having trouble with mathops-test and tandem-test unit test that exercises internal components of CELT codec, please find attached document for each test case failure in details. Also could you please give some inputs on CELT Low complexity code and full version of the code, point me source code to CELT

I wonder whether R provides an interface to access miRecords data. Particularly, I am looking for extracting humans miRNA and target genes sequences. All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords) I would greatly appreciate any suggestion even about other data bases from where it is possible to get the same sort of data. I had a

Unluckily I dela with miRNA files whose name may contain the character "*". Because of the special meaning of "*" I have to remove it. I found out how to make list.files() extract only those file names which contain a "*" Namely: # list.files(pattern="\\*") Now I have to process all files whose name does NOT contain the character "*". I cannot

Thank you for your prompt answer. The breathing signal observations are the amplitude values as a function of time and phase. According to our model the hidden states are the different breathing types. Subjects, whose respiratiion process is regular, are likely to breathe, keeping the same cycle pattern/type, for many consecutive cycles. therefore dwelling in the same hidden state. The more

I'm doing something wrong but the directions I follow seem simple: tar xvfz vorbis-nightly-cvs.tgz (in /root) cd vorbis ./configure make make install There didn't seem to be any unusual output from configure or make, but make install results in: cat install.sh >install chmod a+x install both of these files are empty. The directories /usr/local/bin, usr/local/man and

Full_Name: ivo welch Version: current OS: linux Submission from: (NULL) (130.132.33.212) * In the ?subset page, please add subset( dataframe, select= c(-column1,-column2) ) returns a dara frame that is without columns 1 and 2 . * Also, in ?lm, it would be nice to add a few more words about how to get a residuals vector of the same length as the variable vectors, even if there

Dear R-gurus, Just supose I have a dara.frame that looks like myDF<-read.table(stdin(),head=T,sep=",") codID,namesp,k1,k2,k3,k4 1,spA,2,5,6,3 2,spB,4,5,4,6 3,spC,2,1,5,6 4,spC,5,4,3,2 5,spD,1,2,3,4 6,spE,2,4,3,1 I need to update the columns k1-k4 with the namesp, but considering the math between Kx and codID. My desired output must looks like: codID,namesp,k1,k2,k3,k4

Dear R users, I've written the following functions to implement Silverman's modality test ("Using kernel density estimates to investigate multimodality", J.R. Stat. Soc. B, 43, (1981), 97-99.), and I tested them on the Chondrite data set (Good & Gaskins, J. Amer. Stat. Ass., 75, (1980), 42-56). Values for the critical window width seem OK, which is not the case for the

I am looking for some explanations about the usage of the poorely documented R paclkage Rwave. Has anyone ever tried out its functions for Wavelet Analysis ? Thank you so much. Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[alternative HTML version deleted]]

I keep getting the following error when I look for minima in the series: > aa.peak <- wavCWTPeaks (aa.tree) Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "0")) : invalid 'row.names' length How can I work it around ? Thank you. Regards, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM!

Is there any way to handle errors retuened by R functions ... something like the exception handling in C++ ? Thank you so much, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[alternative HTML version deleted]]

The vorbis FAQ mentions that decoding vorbis should use roughly the same resources as decoding MP3's, but that the current source is not optimized. So what is the current requirement? I have a Pentium 133 with 64 megs and I cannot get .ogg files to play without skipping. I've tried encoding .wav files and downloading .ogg files from www.vorbis.com and playing them on Winamp with

I use FireFox as my favourite web browser on my Mac OS/X 10.5 I double-checked that Java and Java scripts are enabled for FireFox. Nevertheless, I cannot use R on-line search help. I called Apple Tech Assistance but they do not support FireFox. We tried to set Saphari as the favourite browser but evidently R does not support it. Does any one knw of a workaround this annoying problem ? Thanks a