User: Veerendra GP

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Veerendra GP100
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5 years, 2 months ago
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8 years, 9 months ago
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Posts by Veerendra GP

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Extracting strand information from GenomicFeatures transcript db objects
... Dear Hervé, Thank you very much for your email. I am going to update my "GenomicFeatures" right now! Just for your information, I tried using "makeTranscriptDbFromBiomart()", as instructed by you in your previous email. It worked fine! Cheers, Veerendra On Fri, Mar 14, 2014 at 6:46 PM, Herv ...
written 5.2 years ago by Veerendra GP100
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Extracting strand information from GenomicFeatures transcript db objects
... Dear Members, Greetings! I am trying to create a Transcript db object, from the GTF file for Musmusculus transcriptome data available at ensembl FTP site (version 75). ftp://ftp.ensembl.org/pub/release-75/gtf/mus_musculus I am using the function, "makeTranscriptDbFromGFF()" from the " GenomicFea ...
transcriptdb biomart written 5.2 years ago by Veerendra GP100 • updated 5.2 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: Extracting strand information from GenomicFeatures transcript db objects
... Dear Valerie, Thank you very much for the descriptive reply and your suggestion, it indeed was a cryptic error for me but now I understand the cause. Thanks, Veerendra On Wed, Feb 13, 2013 at 12:19 AM, Valerie Obenchain wrote: > Hello, > > Thanks for sending a reproducible example. Sorr ...
written 6.3 years ago by Veerendra GP100
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Extracting strand information from GenomicFeatures transcript db objects
... Hello Everyone! Greetings! I am using "GenomicFeatures" library to create Transcript db objects for the mouse genome. I did it by using biomart, *makeTranscriptDbFromBiomart()* and also UCSC, makeTranscriptDbFromUCSC() functions. As I am interested in the strand information, I tried fetching the ...
transcriptdb biomart written 6.3 years ago by Veerendra GP100 • updated 6.3 years ago by Valerie Obenchain6.7k
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Comment: C: Regarding quantile normalization.
... hi sean, I am sorry the code i mentioned in the last mail was not a running code. here i have displayed the complete running code. library (limma); targets <- readTargets("target.txt") #print (targets); RG<-read.maimages(targets$FileName,source="agilent",columns=list(R="rP rocessedSignal",G= ...
written 8.4 years ago by Veerendra GP100
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Comment: C: Regarding quantile normalization.
... hi sean, I am sorry the code i mentioned in the last mail was not a running code. here i have displayed the complete running code. I have done the quantile normalization before multiple testing. library (limma); targets <- readTargets("target.txt") #print (targets); RG<-read.maimages(targets$ ...
written 8.4 years ago by Veerendra GP100
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Regarding quantile normalization.
... hellow everyone! I will be delighted if any one can help me with this! I am working on a microarray dual channel data, and i need to do a inter array normalization. I have tried with quantile normalization (available in limma package) method but the result i am getting is not satisfactory as the bo ...
normalization limma written 8.4 years ago by Veerendra GP100 • updated 8.4 years ago by Darlene Goldstein230
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help in downloading some packages.
... Hi, I am working on "Microarray Data analysis" using R programming. I need to do some Gene Ontology and Pathway analysis of the extracted genelist. For the same i am trying to download some Packages like - > goTools, topGO for Gene Ontology. > sigPathway for Pathway analysis. But unfortunatel ...
gotools sigpathway topgo written 8.6 years ago by Veerendra GP100 • updated 8.6 years ago by Michael Dondrup550
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help on lowess and density plot.
... Dear all, i need to ask two quections which are in my mind, 1.Wether lowess normalization take in yo account of dye bayes during normalization? 2.How density plots are drawn from MA objects (i.e, after lowess normalization) as it contains only M and A values not R and G values, to draw red and green ...
normalization written 8.7 years ago by Veerendra GP100 • updated 8.7 years ago by James W. MacDonald50k
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Help to confirm Design matrix and Between array Normalization.
... Dear friends, I have DNA differently methylated data of (done with differentially methylated hybridization technique) three cancerous experiments. The experimental design is as follows: Normal vs Tumor: wherein Normal is labeled with cy3 and Tumor is labeled with cy5. Normal vs Pre malignant: wher ...
limma written 8.8 years ago by Veerendra GP100

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For help in downloading some packages.

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