User: Karthik K N
Karthik K N • 200
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Posts by Karthik K N
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... 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 6.7 years ago by
Karthik K N • 200
0
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... 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 6.7 years ago by
Karthik K N • 200
0
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... 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 ...
written 6.7 years ago by
Karthik K N • 200
• updated
6.7 years ago by
Tim Smith • 1.1k
0
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... 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 ...
written 6.7 years ago by
Karthik K N • 200
• updated
6.7 years ago by
Marc Carlson • 7.2k
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... 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 ...
written 6.7 years ago by
Karthik K N • 200
0
votes
1
answer
1.2k
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1
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... 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 ...
written 6.8 years ago by
Karthik K N • 200
• updated
6.8 years ago by
Marc Carlson • 7.2k
0
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... 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 6.8 years ago by
Karthik K N • 200
0
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2
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1.1k
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2
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... 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 ...
written 6.8 years ago by
Karthik K N • 200
• updated
6.8 years ago by
Sean Davis ♦ 21k
0
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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 6.8 years ago by
Karthik K N • 200
0
votes
2
answers
442
views
2
answers
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 6.8 years ago by
Karthik K N • 200
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