search for: micrornas

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 cell1 and high in cell2. I

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the

...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 each...

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

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 used and highly recommended? I googled this topic and found

Hello Sir/ma'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

> On Apr 15, 2016, at 6:07 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote: > > Hi > > Keep your answers to R help (others can help you too) > > From the warning message it seems to me possible that function ReadExi needs to write something to the working directory. As I said I am not an expert in this package, but commands from help > > R>

Hi Keep your answers to R help (others can help you too) From the warning message it seems to me possible that function ReadExi needs to write something to the working directory. As I said I am not an expert in this package, but commands from help R> make.gal.env(galname='galenv', gal.path='Exiqon') R> ebatch <- ReadExi(galname='galenv',

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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")

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