User: Karthik K N

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Karthik K N200
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Posts by Karthik K N

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Comment: C: Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
... Hello Tim, I tried your first suggestion (for chromosome 1). I got an error message as shown below: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 2134 did not have 2 elements Did you see something like this at your end? Thanks, Karthik On Mon, Jul 23, 20 ...
written 7.0 years ago by Karthik K N200
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Comment: C: Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
... Hello Tim, Thanks for the reply. I think this will give the 3'UTRs of all the genes in chromosome 1. How can I get this for ALL the genes in ALL the chromosome instead of repeating the step by changing the chromosome number? Thanks a lot once again. On Mon, Jul 23, 2012 at 5:04 PM, Tim Smith wr ...
written 7.0 years ago by Karthik K N200
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Problems in retrieving 3'UTR sequences of ALL human genes using biomaRt
... Dear Members, I am trying to download the 3'UTR sequences of all human genes from Ensembl Biomart using the package biomaRt. Ideally, after retrieving I want to save these in FASTA format. When I am using the code given below to get 3'UTRs of genes in chromosome 1, 2 and 3 (not sure if this is the ...
biomart written 7.0 years ago by Karthik K N200 • updated 7.0 years ago by Tim Smith1.1k
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Error: Re: Annotation Database for Agilent 8x60K Human Gene Expression Arrays
... Hello Marc, I am trying to create an annotation package for Agilent 8x60K human gene expression array using SQLForge. I have a agilent_ID.txt file with Agilent Probe IDs in the first column and Entrez Gene IDs in the second column. I am using the following code: >library("human.db0") >agil ...
annotation probe affy annotationdbi agi4x44preprocess written 7.1 years ago by Karthik K N200 • updated 7.0 years ago by Marc Carlson7.2k
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BioC package for miRNA target scanning (or displaying results from databases)
... Dear Members, Are there packages for searching miRNA targets in Bioconductor? I Have a list of miRNAs each of whose common target I want to pull out from TargetScan, PicTar, miRanda, miRDB etc. Is this really possible? As a last resort, which BioC/R package can help me search the aforementioned ...
mirna written 7.1 years ago by Karthik K N200
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Annotation Database for Agilent 8x60K Human Gene Expression Arrays
... Dear Members (and especially Marc Carlson), I have few questions: 1. I was wondering whether HsAgilentDesign026652.db is the latest updated database for Agilent 8x60K human gene expression arrays or is there any other file? I have been told by Axel that HsAgilentDesign026652.db cover the oligos u ...
microarray annotation agi4x44preprocess written 7.1 years ago by Karthik K N200 • updated 7.1 years ago by Marc Carlson7.2k
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Answer: A: Access to Source Codes of Packges
... Dear David, Thank you for your help. Can you please tell me how do you exactly edit the source code of a package and the use this 'modified package'? For example, I was wondering if it is possible to add some 'filter by flags' option in limma so that I can filter out probes that do not meet the sp ...
written 7.1 years ago by Karthik K N200
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Access to Source Codes of Packges
... Hello members, I am using AgiMicroRna and Limma packges for analyzing Agilent microarray data. I would like to know if it is possible to have access to the source codes of these packages so that I can better understand what is goind on in the background when we call each functions. Also, is it pos ...
limma agimicrorna written 7.1 years ago by Karthik K N200 • updated 7.1 years ago by Sean Davis21k
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Comment: C: AgiMicroRna and Replicates
... Dear Rich, Thank you so much for your inputs. Regards, Karthik On Thu, Jun 14, 2012 at 7:24 PM, Richard Friedman < friedman@cancercenter.columbia.edu> wrote: > Dear Karthik, > > > On Jun 14, 2012, at 9:45 AM, Karthik K N wrote: > > Dear Rich, >> >> Thanks a ...
written 7.1 years ago by Karthik K N200
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Comment: C: AgiMicroRna and Replicates
... Dear Steve, Thank you for your reply. I have done microarray experiments with pooled samples instead of replicates. I wanted to know if there is any technical difficulty in AgiMicroRna if we have no replicates. Thanks, Karthik On Thu, Jun 14, 2012 at 7:32 PM, Steve Lianoglou < mailinglist.ho ...
written 7.1 years ago by Karthik K N200

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