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 lot for your reply. I am just worried because somewhere I
>> remember reading that LIMMA can't be used without replicates ( in case of
>> mRNA microarray analysis); so just wanted to check if it is the same with
>> AgiMicroRna package also.
>>
>
> I think that LIMMA can be used without replicates but it cannot give you a
> p-value. I suggest
> a minimum of 3 biological replicates per sample.
>
>
>
>> Also, Do you think it is a good idea to  carry out GeneSpring analysis
>> upon the data analyzed by biocondcutor? Will it give any statistically more
>> reliable output that using either of them alone?
>>
>
> I do not know how GeneSpring normalizes Agilent MicroRNA  data but
> AgiMicroRna  is the best way to
> normalize such data described in the open literature of which I am aware.
> The statistical methods in LIMMA are more reliable than those in
> GeneSpring in general. However
> with only one replicate of each condition neither program can give a
> p-value, only a log2FC.
> You can get the same result in an excel spreadsheet,
>
>
>
>
>> Also, since the data from bioconductor has already normalized, if we
>> again give this as an input file for genespring and go on with analysis,
>> then do we need to do normalization step again in GeneSpirng? Won't this be
>> a double-normalization?
>>
>
> I haven't used GeneSpring for a long time. I am not sure what it will do
> to your data.
> If you only have one replicate you might  consider using AgiMicroRNA to
> normalize and Excel to
> compute the log2FC.
>
> Best  wishes,
> Rich
>
>
>
>
>
>> I am new to R/Bioconductor, so any suggestions from you will be extremely
>> helpful.
>>
>> Thanks a lot,
>>
>> Karthik
>>
>>
>> On Thu, Jun 14, 2012 at 7:08 PM, Richard Friedman <friedman@cancercenter.
>> **columbia.edu <friedman@cancercenter.columbia.edu>> wrote:
>> Dear Karthik,
>>
>>       I am pretty sure that AgiMicroRna will normalize one treated and
>> one control. The problem comes later in terms of the reproducibility
>> of the effect, or to phrase it differently, whether the observed effect
>> is a general statement  about the population of treatments and controls.
>> In more specific terms, the subsequent LIMMA analysis will not
>> compute a p-value.
>>
>> With hopes that this helps,
>> Rich
>> ------------------------------**------------------------------
>> Richard A. Friedman, PhD
>> Associate Research Scientist,
>> Biomedical Informatics Shared Resource
>> Herbert Irving Comprehensive Cancer Center (HICCC)
>> Lecturer,
>> Department of Biomedical Informatics (DBMI)
>> Educational Coordinator,
>> Center for Computational Biology and Bioinformatics (C2B2)/
>> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
>> Room 824
>> Irving Cancer Research Center
>> Columbia University
>> 1130 St. Nicholas Ave
>> New York, NY 10032
>> (212)851-4765 (voice)
>> friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu>
>> http://cancercenter.columbia.**edu/~friedman/<http://cancercenter.columbia.edu/~friedman/>
>>
>> "School is an evil plot to suppress my individuality"
>>
>> Rose Friedman, age15
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Jun 14, 2012, at 5:51 AM, Karthik K N wrote:
>>
>> Dear Members,
>>
>> Do we need replicates to carry out analysis with AgiMicroRna package in
>> bioconductor? I have one control and one treated samples. Can I go ahead
>> with AgiMicroRna with these two datasets?
>>
>> Thank you.
>>
>> --
>> Karthik K.N
>>
>>       [[alternative HTML version deleted]]
>>
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>>
>>
>>
>>
>> --
>> Karthik K.N
>> Cancer Discovery Biology Laboratory
>> Division of Molecular Medicine
>> Amrita Center for Nanosciences and Molecular Medicine
>> Amrita Institute of Medical Sciences
>> AIMS-Ponekkara (P.O), Kochi
>> Cochin, Kerala - 682 041
>> +91-484-280 1234 x 8720
>> +91-9400193907
>>
>>
>


-- 
Karthik K.N
Cancer Discovery Biology Laboratory
Division of Molecular Medicine
Amrita Center for Nanosciences and Molecular Medicine
Amrita Institute of Medical Sciences
AIMS-Ponekkara (P.O), Kochi
Cochin, Kerala - 682 041
+91-484-280 1234 x 8720
+91-9400193907

	[[alternative HTML version deleted]]

