search for: mirna

...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 miRNA has been measured on three different arrays and on each array I have 4 replicates for each miRNA, which sums up to a total of 108 measurements. I've the suspect that measurement on the first array are systematically lower than the others so I wanted to draw some line plot where each panel corre...

I have the following files list: > list.files() [1] "Prostate-Cancer_cvs_Dir" [2] "Prostate_Cancer-miRNAs&Genes.Pathway.xml" [3] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir" [4] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir.zip" [5] "Prostate-miRNAs.OrganTargets.txt" [6] "Prostate_Organ-miRNAs-GenesTargets-Dir&qu...

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 RNU48 22.36 3 BC54 miRNA 221 26.49 4 BC54 miRNA 221 26.42 5 B...

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 miRNA 1103243 1103332 + ACC=&q...

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 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() pv <- vector() print(paste(i,&quot...

Hi, I have a question about filterMicroRna in AgiMicroRna package function for filtering probes in Agilent microRNA dataset. >ddPROC = filterMicroRna(ddNORM.micro, dd, control = TRUE, IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 75, limNEG = 25, makePLOT = TRUE, target.micro, verbose = TRUE) If in a dataset there are two or more sample replicates and in the step of

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 look at the database...

Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

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 f...

..., I cannot open it with OpenOffife spreadsheet program and Excel itself cannot separate the columns as it does when a true XLS file is loaded. I tried to read the attached downloaded file through R function "read.xls" and got the following message > read.xls("Prostatic_Neoplasm-miRNAs.Disease-GenesTargets.xls") Error in xls2sep(xls, sheet, verbose = verbose, ..., method = method, : Unable to read translated csv file '/tmp/RtmpPIe3vo/file15d9580e.csv'. Error in file.exists(tfn) : invalid 'file' argument I have tried reading the file through "read.t...

Hi, When a want to use scheduled_task for create a windows task and when i give a AD user, i have this message : err: /Stage[main]/Mirnas/Scheduled_task[test]/ensure: change from absent to present failed: Invalid user: DOMAIN\oper My user domain and the password are correct. I have the same error if i change DOMAIN\oper by oper@domain.com or DOMAIN/oper With a local user, is working, but i need a AD user for my batch to work. Is...

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c&...

Dear Sir: > I am a chinese researcher who interested in miRNA, and I want to use R to analysis my data.I have download R-2.4.0-win32.exe and install it smoothly on my > computer,but when I want to use this software, error occurs,it shows" R for > > windows GUI front-end meet some problems" and the interface closese > automatically, I...

It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA target genes transcription. Each record is made up of a 3'utr identifier <hgnc_id>.<ensembl_id>.<transript_id> followed by the relative 3'UTR sequence. I hoped I cou...

...For CharacterToFASTArecords, the (possibly named) character vector to be converted to a list of FASTA records as one returned by readFASTA" Since I have description and sequnce in separate variables ... I do not know how to use it. zz <- file (filname,"w") write(miRNA.rec, zz, append = FALSE) write(miRNA.seq,zz, append = TRUE) # geneDesc <- paste (">",gene.id, "|", gene.map[i,"ensembl_transcript_id"], sep="") geneSeq <- gene.seq[i,"3utr"] gene.string <- list(desc...

Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A...

...on) or the 2 files compressed in a zip archive. Thank you so much, Maura ======================================================================== ==== Benvenuto in Alice Giga Mail! mauede@alice.it tramite il servizio Giga Mail ha messo a tua disposizione i seguenti allegati: * Prostatic_Neoplasm-miRNAs.DiseaseTargets.xls ( 22773 bytes ) * Prostate-miRNAs.OrganTargets.xls ( 49711 bytes ) per scaricarli, fai click sul seguente link che ti portera' su una pagina dove troverai i comandi per visualizzare o scaricare gli allegati sul tuo PC: http://gigamail.rossoalice.alice.it/messages/readMessa...

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I use heatmap.2(dataset, col=redgreen(50), scale="row"). But I can only see t...

....numeric(geneMetric[,2])~geneMetric[,1]) ? ? listMetric <- as.data.frame(sapply(listMetric,sum)) #returns a dataframe ? ? colnames(listMetric) <- c('cumulMetric') ? ? #return whole list ? ? return(listMetric) } deMirPresGenes looks like this: Gene.ID? ? Gene.Symbol? ? Species.ID? ? miRNA? ? Site.type? ? UTR_start? ? UTR_end? ? X3pairing_contr? ? local_AU_contr? ? position_contr? ? context_score? ? context_percentile 22848? ? AAK1? ? 9606? ? hsa-miR-183? ? 2? ? 1546? ? 1552? ? -0.026? ? -0.047? ? 0.099? ? -0.135? ? 47 19? ? ABCA1? ? 9606? ? hsa-miR-183? ? 2? ? 1366? ? 1372? ? -0.011...