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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

what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
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.
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
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
characteristics of micro business
for teaching engĺish at school how nano technology help us
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
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
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.
what is the actual application of fullerenes nowadays?
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.
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.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
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.
Do you know which machine is used to that process?
how to fabricate graphene ink ?
for screen printed electrodes ?
What is lattice structure?
s. Reply
of graphene you mean?
or in general
in general
Graphene has a hexagonal structure
On having this app for quite a bit time, Haven't realised there's a chat room in it.
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit 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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