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Figure 3

Illustration of the structure of the synthetic data with parameters: p = 3, n = 2, D = 2, N = 3, and Δ = 3.0. The differentially expressed genes are gene1 and gene3. The two different colors of points indicate the two classes of samples: “control” and “perturbed”.

The Characteristic Direction method is represented by a vector in expression space, each component of which corresponds to a gene. We interpret this vector by taking the square of each component to be a measure of the importance of the corresponding gene in the differential expression; the larger the squared component the more significant the gene. In order to determine the appropriate threshold above which to accept genes as differentially expressed we derive a null distribution for the ranks of the squared components as follows:

Generate two random sample means by drawing from the multivariate student t distribution with - 1 degrees of freedom and find their difference.

Calculate the null characteristic direction = Σ Δ

Calculate MathML and rank the components into descending order of magnitude


To compare the real distribution the null we take the ratio: MathML . The simplest and most conservative approach would be to accept into the set of differentially expressed genes all those genes for which the ratio: MathML . A less conservative method to derive the threshold from the data is to consider the inflection in the curves which can be isolated with the cumulative distributions.

Figure 4

Illustration of gene set enrichment with the characteristic direction concept. a) Similarity between two perturbations can be interpreted as the angle subtended between two characteristic directions. b) Gene set enrichment analysis can be formulated as the principal angle between the characteristic direction and the subspace spanned by the genes in a gene set.

We collected 73 experiments from GEO (Additional file Katy Perry Womens The Matilda Slipper Forest Green YCu1Eg
: Table S1) which contain expression data for control verses TF perturbation with at least three biological replicates in each of these classes. The TF perturbations consisted of knockdowns (32), knockouts (29), over-expressions (5), and other types of perturbation (7) such as partial mutations for example. A complete list with the details about these experiments can be found in the Additional file 1 . We extracted processed expression values from the SOFT files downloaded from the GEO database. For each experiment, we compared control and perturbed classes with four different methods: the fold change, Welsh’s t test, SAM, and the geometrical approach described above which we shall refer to as the “characteristic direction” approach. Each experiment and method pair resulted in a ranked list of all genes on the particular array chip in order of their estimated significance in the differential expression.

In any case, I notice, at 61, when I spend a lot of my time sitting on this same sofa writing and groaning about writing, how much these guys love to move. The pregame exercise look like dancing, or horses out to pasture. Heels up. I think about how I creak to stand sometimes – it’s renewed inspiration to get going.

And so gorgeous all of it. They call soccer “The Beautiful Game;” I just see beautiful players. I mean in the usual way, of course, so many handsome men in one place. Such a plus. But also human beings in comfortable clothes moving as we were born to.

I know there’s all kinds of non-beautiful in soccer’s history, corruption, injury, violence. But since no one will die or be left starving if I stick my head in these particular sands, I claim impunity.

Match time. I hope you’ve got a moment of indulgence lined up, one that makes you happy and hurts no one at all.

Have a wonderful weekend.

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What A Polished Tomboy Wants To Wear To Those Daytime Events, Or, Saturday Morning at 10:01am

( Note: Although I no longer monetize new posts on this blog, the images below are pay-per-click. That’s because the tool I use to search for ideas, ShopStyle Collective, automatically includes theirlinks in generating the widget. It would take me forever to try and replicate this what with Photoshopping and cutting and pasting. Please forgive my inertia.)

So, daytime events?

My issue is as follows:

Flowing or floral dresses are not me; fancy structured trousers are for work, not parties.

Which lands me, paradoxically, for daytime celebrations, in a world of structured dresses and flowing or floral trousers. Well all right then!

Here are some dresses I quite like. What do you think? A couple of florals because never say never. Comme des Garçons animé for our Artsy Cousins, Diane von Furstenberg or Victoria Beckham for the Grande Dame. She’ll change for dinner, by the way. The Veronica Beard ruching, not before noon.

My favorite is that blue Max Mara Weekend shift, because, blue. With low block-heeled sandals which I happen to own.

And what about flowing trousers? That’s what I ended up wearing to my daughter’s graduation. And this believe it or not is the best photo I have. (Yes I got a haircut, Nike Womens Free 50 Print Nbl Prpl/Smmt Wht/Pnk Fl/Vltg Running Shoe 95 Women US tS5on6MFl7
was unsupportable.) Patent leather J. Crew slippers and belt. SJP by Sarah Jessica Parker Womens Gelsey Ballet Flat Superior dVfvoC

Well, maybe the trousers are not so much flowing as purchased 10+ years ago for work when Armani was wide-leg friendly. I would like to up the festive quotient.

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This article presents a view of this issue that is often overlooked – that the policies universities adopt relative to math requirements can be seen as civil rights issues. As a Latino college math professor who started his training at Cal State Northridge, this is an important issue for me. In fact, I spent three years as an employee of the Carnegie Foundation and worked on both Statway and Quantway in a variety of ways. For the last four years, I’ve been back at work as a full time professor of math, and have been working hard with colleagues at my own college to totally re-invent our curriculum so that non-STEM students have quality, rigorous, and shortened pathways to complete their associate degrees.

I’m not alone! All over the country, hundreds (probably thousands) of math faculty are working very hard on this challenging issue. A lot of the hard, time-consuming work on Statway and initiatives like it has been done by math professors who actually do believe our non-STEM majors are perfectly suited for “meaningful civic engagement” and absolutely deserve a college education and degree.

This entire article frames the issue as one of policy at CSU. Then, only at the end, the author implies that “many” math professors are a big part of the problem. And that may be true to some degree – some math faculty hold on to beliefs that get in the way of clearing obstacles for students to complete their education, as do many other faculty, factors, and policies.

But the article also states that across the country, students who are “given the chance to enroll directly in college statistics, or take a remedial course on quantitative reasoning skills better aligned with statistics” are “succeeding at far higher rates than those forced to take algebra courses.”

Who do you think is giving them this chance? It doesn’t appear out of nowhere. Many administrators, curriculum writers, non-profits and, yes, math faculty, have done the hard work to make these options available to students. I think it’s important to keep in mind that “many” math professors are on the front lines of addressing this issue by working on and with initiatives like Statway, creating and testing new curriculum, learning new and more effective pedagogical practices, engaging with four-year institutions to ease transfer options, etc. Indeed, “many” are doing their part. Taking a snarky swipe at math educators at the end, without providing a balanced picture of their work to remedy this situation, doesn’t make much sense. Nor does it seem particularly productive.

I was at a restaurant some time ago. The waitress accidentally charged 10% tax on the bill instead of 8%. And she had lost the pre-tax cost of the dinner. No one knew how to figure out the correct amount for the bill. It was a question in basic algebra but no one knew how to come up with the correct amount for the bill. Finally it was brought … Read More

I was at a restaurant some time ago. The waitress accidentally charged 10% tax on the bill instead of 8%. And she had lost the pre-tax cost of the dinner. No one knew how to figure out the correct amount for the bill. It was a question in basic algebra but no one knew how to come up with the correct amount for the bill. Finally it was brought to the attention of the restaurant manager and he figured it out. It is foolish to say that basic mathematical skills are not part of everyday life. Moreover, this article makes it sound like requiring knowledge of low-level high school mathematics is an indictment against people who are not mathematically savvy.

There is a reason to know basic high school mathematics. The higher level courses like college algebra, calculus, statistics, freshman physics, freshman chemistry all rely on the basic mathematical skills from high school mathematics. If students wish greater insight into the world and the universe we live in, they will not achieve it without such basic mathematics. Such students can make it through these courses with a great deal of anxiety but they won’t have actually learned anything – they will not have any greater insight. These courses will be painful and will serve only as a right of passage – not as a path to any kind of insight or enlightenment.

It is emotionally painful to see many students pay tens of thousands of dollars a year in tuition, not to actually learn anything. Education is not supposed to be a survival contest. It is to bring about a deeper understanding of oneself, the world and the universe we live in. Of course it is to learn necessary technical skills for one’s career. Education has to keep a balance between pragmatism and world view. It is wrong to think of education solely as a means to make money. Trade schools exist for that. They serve a purpose – as important as any. If the individual wants only that, then this option exists. But that is a distinct purpose and different from that of a college or university.

Even the natural sciences – biology in particular – are becoming more mathematical, as the growing fields of biophysics, bio-mathematics and bio-statistics are making increasingly greater contributions to the field. The long unsolved protein folding problem is now understood having applied statistical mechanics to the entropy and free energy of the proteins. Mathematics continues to make important contributions to fields of study and to society in ways that were previously not envisioned.

Carl Sagan pointed out that our economy is becoming completely dependent on technology but society is becoming more technologically ignorant. He argued that such a schism could ultimately be catastrophic.

On top of this, many colleges have tutoring centers where the student can get one on one help. These centers can review the class notes with the student, can review homework with the student and most importantly provide a channel for communication and personal attention. Many centers provide feedback to the professors so that they are aware of the efforts of the students.

As with everything in life, this is a question of responsibility and accountability. There is cause and effect. If a student neglects education from early on, there will be a deleterious outcome later.

And regarding the concepts of responsibility and accountability, this article is blaming the “institution” and the “collection of math professors” for the indolence of the individual. There are two ways to make it at anything. One is to be blessed with natural talent, the other is through hard work. This article condones displacing responsibility for the individual and transforming into blame of the institution. And the reader will hopefully notice the hypocrisy in marginalizing an entire sect of society (the professor or the math professor). You cannot get justice nor an efficient system by continually displacing responsibility from one group while blaming another. This is a classic case of playing victim to avoid responsibility. Playing victim has nothing to do with justice. It is always about gaining power.

To paint this topic with such broad strokes is a deception, a play at sophistry and manipulation.

Let’s understand that advanced math has been used as a gatekeeper by numerous departments in the academy when each respective department/field should have field-oriented assessments that evaluate students’ abilities when enrolled in the major itself. It’s about understanding disciplinary literacy as tied to each field or subfield. The community colleges seem to get it. Perhaps one day the same will be true for those in the UC or CSU system.

Hasn't anyone taken the time to think that maybe it's just on the student? I'm currently a fourth year at UCSB and a transfer student, and I started off in trigonometry, and that was a tough class. But guess what: I worked harder than I thought I could and I passed. There are so many resources out there for students to succeed including detailed solutions for students to look at. To the author, I know … Read More

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