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What are the spot numbers for the three highest ranking spots?

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What are the "R/G Normalized (Mean)" values for the three highest ranking spots?

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Does it change the ranking of the spots to use the log transformations of the ratios instead of the ratios?

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To demonstrate a different method of visualizing and analyzing microarry data,take a look at the MIT Cancer Genomics Microarray Data Sets . Scroll down to the section entitled "Gene Expression Correlates of Clinical Prostate Cancer Behavior".Click on the first data set, for Prostate tumor and normal samples, entitled "Prostate_TN_final0701_allmeanScale.res". This data set originates fromAffymetrix chips. In this case, the signal is recorded as "A" for absent, "P" for present, and"M" for marginal, as determined by the Affymetrix GeneChip software. The numerical values are scaled average difference units for tumor vs. normalprediction, and these values are also generated by the Affymetrix software. A more complete discussion of gene expression data analysis for AffymetrixGeneChip Arrays can be found at the Affymetrix web site .

So far, the discussion has been primarily about visualizing and quantifying the fluorescence signal from a microarray experiment. However, analysis ofgene expression under experimental conditions versus reference conditions requires determining whether observed differences are significant or not.There are many sources of noise and variability in microarray data, including experimental sources such as image scanning inconsistencies, issues involved incomputer interpretation and quantification of spots, hybridization variables such as temperature and time discrepancies between experiments, andexperimental errors caused by differential probe labeling and efficacy of RNA extraction.In addition, as the size of the sample increases, so does the probability of finding some large differences due to chance. Therefore, statistical analysisis required to show that gene expression differences are real.

There are some complex problems underlying statistical analysis of microarray data, primarily related to the fact that the number of samples is very, verylarge, but the number of times that each measurement is repeated is comparatively very small. (This is due mostly to cost and time issues.)Also, the simplest statistical techniques commonly assume a normal distribution, which cannot necessarily be assumed in microarray experiments. For a detaileddiscussion, D. K. Slonim (3) has authored agood review of the most current approaches to gene expression data analysis.

This tutorial will provide an oversimplified example of the type of statisticalanalysis that needs to be applied to microarray data, using the t-test. For a given gene, A, the gene will have two associated vectors:{a(ref)1, ..., a(ref)n} and {a(exp)1, ..., a(exp)n}, where a(ref) contains n measurements of expression levels under reference conditions and a(exp)contains n measurements of expression levels under experimental conditions.

Questions & Answers

anyone know any internet site where one can find nanotechnology papers?
Damian Reply
research.net
kanaga
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
Daniel
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
Maciej
characteristics of micro business
Abigail
for teaching engĺish at school how nano technology help us
Anassong
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
NANO
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
s.
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
Tarell
what is the actual application of fullerenes nowadays?
Damian
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
Tarell
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
Virgil
is Bucky paper clear?
CYNTHIA
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
NANO
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Harper
Do you know which machine is used to that process?
s.
how to fabricate graphene ink ?
SUYASH Reply
for screen printed electrodes ?
SUYASH
What is lattice structure?
s. Reply
of graphene you mean?
Ebrahim
or in general
Ebrahim
in general
s.
Graphene has a hexagonal structure
tahir
On having this app for quite a bit time, Haven't realised there's a chat room in it.
Cied
what is biological synthesis of nanoparticles
Sanket Reply
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
China
Cied
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
Porter
many many of nanotubes
Porter
what is the k.e before it land
Yasmin
what is the function of carbon nanotubes?
Cesar
I'm interested in nanotube
Uday
what is nanomaterials​ and their applications of sensors.
Ramkumar Reply
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Good
Berger describes sociologists as concerned with
Mueller Reply
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Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
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