User: neeraj rana

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neeraj rana100
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Posts by neeraj rana

<prev • 10 results • page 1 of 1 • next >
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significant test when number of sample are only two???
... hi i did two color array (agilent 44K two color) .one sample with two replicate. which test or algorithm can i use to find differentially regulated genes in R package. i have one samples with two techincal replicate: 1.normal = cy3 treated= Cy5 = Cy5/Cy3 2.normal= Cy3 treate ...
written 7.5 years ago by neeraj rana100
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limma matrix design for biological replicates.
... hi, i am doing analysis for 10 breast cancer arrays (two color Agilent4x44 arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are biological replicates ,means all 10 arrays have been prepared from 10 different patients. there are two categories as nod negative and nod positive.Five arr ...
cancer breast limma written 8.9 years ago by neeraj rana100
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Error: could not find function "mixedModel2Fit"
... hi i am getting follwing error in my analysis. > corfit <- duplicateCorrelation(MA.bn, ndups = 1, block = biolrep) Loading required package: statmod Error: could not find function "mixedModel2Fit" In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logi ...
written 9.2 years ago by neeraj rana100 • updated 9.2 years ago by Sean Davis21k
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Error: cannot allocate vector of size 13.7 Mb
... hi ,, i installed R.10.1 for windows in my sytem.I am analysing agilent one color array data by using package "Agi4x44preprocess".i got the follwoing error which i am facing the very first time. > CV.rep.probes(dd, "hgug4112a.db", foreground = "MeanSignal",raw.data = TRUE, writeR = FALSE, targe ...
written 9.2 years ago by neeraj rana100 • updated 9.2 years ago by Sean Davis21k
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AgiMicroRna package is not available at bioconductor or not in active form???
... hi, i need to analyse Agilent microrna microarray by the package AgiMicroRna ,i tried it to intstall but the msz came > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safe ...
microarray microrna written 9.2 years ago by neeraj rana100 • updated 9.2 years ago by Sean Davis21k
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within array normalization for one color agilent array.??
... hi, In the package Agi4x44PreProcess I took the expression value as *MeanSigna*l, then by the method *BGandNorm,* the background subtraction and the normalization between the array is done.But the array should be normalized within the array also first.This the script what is given in Agi4x44PrePro ...
normalization agi4x44preprocess written 9.3 years ago by neeraj rana100 • updated 9.3 years ago by Sean Davis21k
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what does mean of Densities on y axis in the graph generated by plotDensities
... hi i generated one graph by using command plotDensities(MA) for agilent two color array.but i could not understand what does mean of Densities using on y axis. Can you help me please to understand the graph,about what exactly on x axis and what is on y axis. thanking you, NEERAJ RANA JRF ,INDIAN ...
graph written 9.3 years ago by neeraj rana100 • updated 9.3 years ago by Saroj K Mohapatra400
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what is meaning of NA in M values
... hi, i normalized two color agilent array and when i extract the normalized M values ,in the file there NA is written instead of values for some genes.What does that meaning. [[alternative HTML version deleted]] ...
written 9.3 years ago by neeraj rana100 • updated 9.3 years ago by Heidi Dvinge2.0k
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#how to filter bad spots from two color agilent array,
... hi, I am working on two color 4x44Agilent array.I normalized the data with Bioconductor,I used the following scripts to normalize the data.i want to filterout the spots which are not good to be analysis across the array.how can i filter the spots which are having the negative value after backg ...
normalization written 9.3 years ago by neeraj rana100 • updated 9.3 years ago by Sean Davis21k
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agilent reading array data.
... hi, when i am using agilent data to read in bioconductor in Agi4x44PreProcess package i am getting following error.Is there any solution for this error. > dd_ayur=read.AgilentFE(targets_ayur, makePLOT=FALSE) Read US83000164_251485049982_S01_GE1_105_Dec08_1_1.txt Read US83000164_251485049982_S ...
written 9.4 years ago by neeraj rana100

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Popular Question 7.5 years ago, created a question with more than 1,000 views. For what does mean of Densities on y axis in the graph generated by plotDensities

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