search for: mirnas

Displaying 20 results from an estimated 26 matches for "mirnas".

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2011 Oct 10
3
Superposing mean line to xyplot
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
2010 Jun 10
1
selecting and excluding files through a pattern
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&quo...
2009 Apr 28
0
problems understanding error term in aov()
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 BC...
2011 Jun 27
1
create a new data frame after comparing two columns of the previous data frame
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
2018 Mar 21
1
Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository
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
2011 May 31
2
correlatation matrix
...nes out of ", nrow(dat.m),sep="")) cr2 <- cor.test(as.numeric(dat.mi[i,]),as.numeric(dat.m[k,])) cr <- c(cr,cr2$estimate) pv <- c(pv,cr2$p.value) } cor.mat <- cbind(cor.mat,as.vector(cr)) pval.mat <- cbind(pval.mat,as.vector(pv)) } The columns in the output represent miRNAs and the rows mRNAs. The code works fine but takes ages (about an 1.5h for generating a 169x20043 matrix) so I wonder if there is a more efficient way of doing this calculation? Best wishes Kristian ________________________________ Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundh...
2011 Jul 28
1
filterMicroRna function: Sample replicates in preprocessing Agilent miRNA dataset
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
2009 Jun 16
2
R and miRecords
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
2009 Jun 23
2
question about package biomaRt
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]]
2010 Feb 02
2
finding files whose name does NOT contain a given character
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
2010 May 25
2
how can I read a non-standard XLS file
..., 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.ta...
2012 Jun 30
6
Scheduled_task + ad user
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...
2009 Sep 29
4
How can I avoid a for-loop through sapply or lapply ?
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&q...
2006 Nov 06
1
about R install
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 don't know what happen.
2009 Jul 16
0
how to use writeFASTA in modality "append"
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
2009 Jul 17
0
How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...
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
2010 Feb 25
1
taking the median across similar data
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 2.3 2.4 2.5 A
2010 May 25
0
Follow-up: how can I read a non-standard XLS file
...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/readMessag...
2008 Oct 14
1
A question about Heatmap for data with just 2 columns
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
2010 Dec 17
1
help with function
Hello List I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R. I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ?