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Figure 2.

False color image of raw intensities in the reference channel. Columns represent arrays and rows represent spots. Only human microRNA spots are shown. The intensities have been location- and scale-transformed within each row (spot) to lie between 0 and 1; this enables comparison across arrays. Other transformations are possible, and give similar results. There are two interesting features in this plot. First, there is a banding pattern of high and low intensity on alternate arrays. This is presumably due to the fact that two arrays are hybridized on each slide. Second, the last six arrays, run on a different day, have consistently higher intensity, suggesting a batch effect. This effect is also seen in Bruno Magli Silico Clearance View Pay With Paypal Cheap Price swx2xrcvI
.

We use this graphic to demonstrate the presence of a batch effect in our experiment. There are two well-defined batches: Arrays 159–184 were labeled on 4/13/07 and hybridized on 4/16/07 (159–182) and 4/17/07 (184). Arrays 207–213 were labeled on 5/5/07 and hybridized on 5/14/07. The arrays from the second batch (207–213) have larger intensity in the green channel. The banding pattern visible in this figure is presumably due to the fact that two arrays were printed on each slide.

Other plots designed to highlight this batch effect can also serve as diagnostics for assessing different normalization methods. Cheap Sale Visit Exclusive Sale Online Steve Madden Hest 6 Get To Buy Cheap Online Outlet Online Clearance Best Place ZJIktsX8
, which encodes a pairwise distance between all arrays, is an example of such a plot. Another example is etnies Jameson SLW Cheap Sale Footlocker For Cheap Best Buy Outlet Get Authentic wXxes9zddr
, which plots the estimated densities for the green channel log 2 intensities. The two batches are indicated by different colors in Philippe Model Paris Lamine leather sneakers Many Kinds Of Zb2GbF
, and a visual separation of the two batches is readily apparent in the densities for the unnormalized intensities. The separation is removed by all three normalization methods considered in this article (see the next section), but with some differences in behavior for low intensities. AIR ZOOM VAPOR X HC Multicourt shoes white/black vast/grey summit white 2018 New oVxO4orQA
also serves as a diagnostic of array quality; had there been any bad arrays, one or more of the corresponding density estimates are likely to have been aberrant.

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Figure 3.

Histograms (kernel density estimates) of log intensity in the reference channel. The rows correspond to different types of probes, and the columns represent the different normalization methods used. Colors distinguish the two batches, and show a systematic upward shift in the second batch. All normalization methods appear to rectify the batch effect for high intensity spots, but have different effects on the low intensity spots.

Normalization is an essential preprocessing step in the analysis of any microarray experiment. Its primary purpose is to try to ensure that the observed between-array differences are due to biological phenomena, and not due to artifacts that arise due to differences in handling or processing of the samples. Normalization of microRNA microarrays is problematic primarily for two reasons. First, the number of microRNAs measured by the arrays is fairly small, numbering only in the hundreds ( XA PRO 3D Trail running shoes mykonos blue Official Cheap Price Discount Cost Free Shipping Online Brand New Unisex Sale Online Discount Codes Really Cheap laPwDoWr
). Second, even among the measured microRNAs, only a small number are expressed at all in a given tissue, and consequently, most of the spots on the arrays cannot be used for normalization. In other words, the usual normalization assumptions do not apply. A careful analysis requires the development of a reasonable normalization strategy, as well as diagnostics that can be used to assess the performance of potential normalization strategies.

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The sweeping staircases and stately elegance of the historic Old Capitol is the ideal backdrop for a picture-perfect wedding. Located in the heart of Iowa City, the building served as the state of Iowa's firstcapitolfrom 1846 to 1857 and became a National Historic Landmark in 1976.The Old Capitol's dome is featured in the University of Iowa's logo and remains one of the most recognizable landmarks in the state of Iowa.

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IMU Main Lounge

The Main Lounge is the perfect location for your wedding ceremony or reception of any size. Continue reading...

IMU Second Floor Ballroom

The spacious Second Floor Ballroom in the University of Iowa's Iowa Memorial Union with its gorgeous woodwork and stunning stage is a beautiful spot for your wedding reception or ceremony. Continue reading...

Danforth Chapel at IMU

This charming 1950's non-denominational chapel adjacent to the Iowa Memorial Union and the beautiful Iowa River is perfect for an intimate wedding ceremony. Continue reading...

IMU North River Terrace

New in 2015, the North River Terrace at the Iowa Memorial Union is a beautiful 6,000 square foot space overlooking the Iowa River and IMU Amphitheater. Continue reading...

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