search for: microrna

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 per array or the mean of all the controls per array. The gal

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...

...y 4: package 'IRanges' was built under R version 2.9.0 and help may not work correctly 5: package 'CORNA' was built under R version 2.9.0 and help may not work correctly 6: package 'GEOquery' was built under R version 2.9.0 and help may not work correctly 7: package 'microRNA' was built under R version 2.9.0 and help may not work correctly 8: package 'Rlibstree' was built under R version 2.9.0 and help may not work correctly > I am stuck. Which packages am I supposed to install again ? Maybe shall I get rid of R 2.10.1 Patched and restart from scrat...

...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 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 eac...

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 ar...

Dear R users, I have a microRNA (similar to microarray) data set with gene expressions and group variables. I'd like to perform (class) prediction analysis to see which genes or gene sets predict the group variable well. I'm at the beginner level. Is there any free software in R or in point/click format that is commonly...

...am, Greetings for the Day ! I am Jyoti Sharma, from India and recently start working on R. I am new in this field and my knowledge is not up to the mark, so if I sound dumb then please forgive me. I tried to read some text file in R so that I can do further analysis on those files. All files are MicroRNA dataset and in exiqon format. When I write function ReadExi and path of my file gives me error - Error in a file(file, "rt") : cannot open the connection. I put a file in the same directory too, even then also it is not working. Can you help me on this issue?? Is there any issue with GAL...

...uot;Exiqon") : Cannot find GAL file. The package documentation mentions a file named GSE20122_RAW.tar at (http://www.ncbi.nlm.nih.gov/geo/) You can find this at an NIH website: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20122 . Status Public on Feb 02, 2010 Title Vitamin D and microRNA Expression The file is linked to at the bottom of that document. It's 87.7 Mb and only expands to a directory slightly large, because the contents are all gzipped. The server is reasonably fast so download only takes a few minutes. The documentation then describes the process for extracting te...

...> I am Jyoti Sharma, from India and recently start working on R. I am new in this > field and my knowledge is not up to the mark, so if I sound dumb then please > forgive me. > > I tried to read some text file in R so that I can do further analysis on those > files. All files are MicroRNA dataset and in exiqon format. When I write > function ReadExi and path of my file gives me error - Error in a file(file, "rt") : > cannot open the connection. > > I put a file in the same directory too, even then also it is not working. > Can you help me on this issue?? Is...

...gy and Bioinformatics The Paterson Institute is a leading cancer centre of excellence core-funded by Cancer Research UK and is an Institute of The University of Manchester. We are seeking motivated scientists to join our team and develop new techniques to explore the biological processes (such as microRNA expression and alternative splicing) involved in the regulation and control of gene expression, and to develop a better understanding of how these processes are altered in cancer. Computation Biologists ---------------------- Two positions are available for postdoctoral researchers with experience...

Hi everyone, I am writing a simple script to read in a data file, search through the data file for an exact character match for a microRNA name, subset those rows, and aggregrate a dataframe with those subselections all in a for loop. This is what I have so far: #READ IN DATA file1 = "C:/Desktop/mirtarget2_predictions.txt" data = read.table(file1, header=FALSE, sep="\t") colnames(data) = c("mir", "g...

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't generate more clumsy website addresses .... Sorry for that. Thank you in advance, Maura tutti i