arraysearch

So I've had, over the last couple of months, lots of new people add me.  I don't know if you're here for the graphics or for the random (I'm guessing graphics) but I'd LOVE to know a little more about you than I can discover stalking your profiles!  So, wanna introduce yourselves?

( if yes, riddle me this.... )

and now I have that song in my head ... getting to know you.... getting to know all about you....getting to like you....getting to hope you like me....

ETA: or maybe i should have titled this "come out, come out, where ever you are!"

More 'recs' (some are yuletide, some are not.... )

What Eli and Oskar Do on their (first) summer vacation (Let the right one in)
Authoress did such a lovely job of capturing Oskar's innocence and confidence, his certainty now that he has Eli, no matter how exactly they're going to keep having each other.  I love that he's the one who is rewriting traditions for her, seeing birthdays and celebrations and reasons to go on that are more than drudgery and duty.  It's interesting because I'd always assumed Håkan was a little boy once who fell in love with Eli, and then grew up, and so part of the chilling thing with Oskar is that he is part of a cycle for her -- but the authoress turns that on it's head and creates something that has the same eerie transcendent power as the movie. 

I can't turn this around (Kris/Adam, AI season 8)
I can't decide if I like this one or not because Adam has amnesia and forgets Kris, his best friend.  I generally like amnesia fics, and I loved the length of this one, the slow remembering, etc, but ultimately ... it's kind of sad that Adam, in the wake of his own success, seems to have turned into kind of a cold guy. Of course, the memory!less Adam isn't a cold guy at all, and so he's loveable and sort of bewildered, and that's nice and he never goes away .... so you don't ever have to see the 'cold'Adam, but it makes me wonder.

D (Chris Pine/Zach Quinto, Star Trek RPS)
Absolutely hilarious 'straight boy doesn't know he's pining until he does' story - Rageprufrock is one of my favorite authors in the Merlin fandom, and I couldn't resist this co-written story.  It's crack, pure crack, which is how I love my RPS best.

Zen and the Art of Scheming (Eric/Vince, Entourage)
The note is 'Vince loses his Zen, it's all E's fault, and Vince is simply not going to put up with it.' And I love the fic in this fandom -- it's all about the fact that it's a little scary tipping over that edge from friendship to lovers, but it comes with the realization that, on some level, that's what's been happening all along.

Click for larger image

Date: The waning hours of December 31, 1939

Location:. Washington, D.C

Now that I'm considering myself more of a multifandom girl, I'm quite enjoying Yuletide fics, which are all pretty awesome in their wonderfulness. And I have some recs (pre reveal). It's kind of weird to go "oh, hey, those books were great! and yes! fanfic!" but glancing down the list that's kind of what I've done....

Make a Home, Invite You In Tony/Lee (Tanya Huff's Blood/Smokes series)
Great mystery element, but the best part is the back and forth of the Tony/Lee relationship, with some Henry thrown in for good measure. It's really quite cute and nabbed me from the very first second, and I read with a smile on my face the entire time. They start out house hunting, but find a little trouble in the process, and I kind of adore all of the interactions between not just Tony & Lee (although I love those too) but also between the two and all the other characters.

They Come In Threes Kris/Adam + Merlin
Adorable mixed-up mash up of Merlin being stuck in a bottle by the dragon and Adam getting him as his horribly bad not very good genie. It all works out in the end though, which makes me totally happy (and besides, the author manages to draw decent parallels between Merlin/Arthur & Kris/Adam, which is kind of amusing). It made me grin the entire way through it.

If on a Yuletide Morn, a reader not bad If on a winter's night a traveler fic.... Really well captured Calivino tone, if you like that kind of thing. REALLY kind of awesome.

kind of insane kris/adam where adam's an angel.... yes, a jewish angel.

really hot and lovely Vanyel/Lendel from the Valdemar series (first time)

cute (although not much of a mystery) Tony/Lee (Tanya Huff's Blood/Smokes series)

really adorable Bradley/Colin (Merlin) with the line "Bradley wants to just kiss him right there - to taste the joy right off his mouth - " just stunning.

pranking Bradley/Colin one-upping-each other into love/a relationship

To a Place we Never Kept Vince/Eric - Entourage
Pre-series road trip of the boys from Jersey to CA. I honestly don't remember if it does a good job fitting in with cannon or not (having seen the series but not looked at it with fandom eyes at the time), but I really love the tone of this fic. For some reason Entourage fics seem to have an awesome banter/guys messing with each other/easy kind of tone, and then they also happen to have two best friends who have grown up in each other's pockets ending up together (ish). This one doesn't disappoint.

Happy Boxing Day!  Which, while I don't actually 'celebrate' per se, has been spent much like many other boxing days - we haven't done much.

We had a lovely Christmas - low key, low pressure, scrumptious, with a couple of strange contretemps.  ( Like poor Neil scalding himself while cooking bacon )

And in the grand tradition of Kate & her Mom, we went and saw It's Complicated today (Sherlock Holmes is next, but Monday night) and had a grand time.  My mom is kind of adorable at movies, and we laughed out loud, which is a good sign, even if i wouldn't necessarily say 'oh, go out and watch it!' to anyone who didn't already like that kind of movie.  Steve Martin was pretty awesome in it though, and very understated, which was kind of cool.

Finally though, tomorrow we're going to be frosting Christmas cookies!  And you may be wondering, why do we have Christmas cookies to frost?  Well, because we didn't stress about making a ton of them before christmas... and now we have the leisure to play without the pressure.  I kind of like this whole relaxed holiday thing.  Much easier on the brain ;)

I hope all of you who were celebrating holidays enjoyed them all vastly.  And those who don't celebrate, I hope you all are having lovely weeks and weekends too!

This is the gene regulatory network ARACNE inferred from the top most 50 expressive genes (as measured by their L2 norms across the sample space):


Click for larger image


Gene 25127_at appears to be a major regulatory gene, so I will check and see what else is known about it.

I also have generated network adjacency matrices for the top 200 and the top 1000 genes as ranked by their respective L2 values, but the network graphs are pretty unwieldy to work with. This graph was generated using Cytoscape - which is a very cool program with a lot of plug-ins, and I am still working my way around it.


More ARACNE results to be forthcoming. The program also comes with Matlab scripts to estimate optimal parameters for a given dataset, and I will run these the next time.

Click for larger image

Date: circa 1925
Location: Washington D.C.
Description: The Western Electric Co. annual office Chrismtas Party

Click for larger image

Date: circa 1920
Description: "Margaret Clark" A Christmas Tree with all the trimmings. And a Buick. Harris & Ewing Collection glass negative
Location: Washington, D.C.

I was trying to find other pictures of the woman in this post, and so far this is what I have come up with.

( More under cut )

It may have been a turbulent flight last night (all the hot air kept us bipping and bopping all over the sky.... they didn't even give us drinks), but we made it safely back in time to say goodbye to D (she left early this morning to visit her other relatives for xmas), and to collapse after our not terribly long but kind of lovely busy day.

( and oh my god I missed home )

I can't believe I had the hubris to do this, but my mom and I visited with my gradeschool music teacher (she's the one who cast me in the lead in our Nutcracker Play in 5th grade.... and I got to do the HMS Pinafore too) and I pretty much talked about myself the entire time.  ( It was a little strange, but also very cool )

The christmas luncheon we were supposed to go to turned out to be scheduled for after 3 pm (and we both needed to pack after 1:30), and so to make up for it we went out with my mom's friend for the best hamburgers in the county.  Diet, schmiet.

Today has been a day of ... well, we attempted to buy presents, we really did.  ( We ended up getting a ton of cheese )

Tomorrow we're off to do even more shopping (those last minute purchases are the most important, really!) and to buy food for Christmas Eve and Christmas Day dinner.

I hope all of you are having fun, smiling, or generally enjoying your evenings in some way....I'm pooped but I'm happy with mine :D

Deleted gene 245127_at (line 3640) from the dataset. ARACNE cannot run if there are missing values. And for some reason across more than half the experimental samples, no expression values exist for this gene. Weird.

Because the atgenexpress dataset is so huge, I have been trying to filter out genes which are not expressed across any of the samples. To this end, I have made use of the mas5calls function in the affy library of R which you get when you install the Bioconductor package. This function performs the Wilcoxon signed rank-based gene expression presence/absence detection algorithm on the microarray data. So in addition to ending up with an Excel file containing gene expression data (the rows are the genes and the columns are the experimental samples), you end up with another Excel spreadsheet of the same size, where in place of each expression value, there is now either the letter P, M, or A. P = present, M= marginal, A = absent (indicating whether the gene was detected or not in the microarray).

My first thought was to use this as a way to filter out genes. By summing the Ps, Ms, and As along each row (gene), I formed the ratio: R = P/(P+M+A). Then sorting the genes from largest to smallest by this value would give me the genes which were detected the most frequently. Genes which have R = 0 I am obviously not interested, so I deleted these from consideration.

There are other factors to consider though. For one, a gene which is highly expressed in one or two samples and could play an important role in the the genetic response of Arabidobsis to a stimulus could be important as well - but have a low R value. If I just filter by R-value, I am only catching those genes which are highly expressed across all experiments. I need to consider the standard deviation of each gene.


I am also interested in the L2 norm value of each gene. Viewing each gene as a vector containing expression values for each sample, I calculate the L2 norm. This is also a way to rank genes.

So there are in fact three ways to rank genes in terms of importance (by L2 norms, standard deviations, and their R values). I am working on a way to link them together into one metric. Below are scatterplots of the various interactions.



Click for larger image

Conclusions:

The linear relationship which appears to exist between the L2 norm and R was kind of unexpected. The mean of all the L2 norms for the genes is 208.5677, and so the concentration of genes near the lower left-end of this graph also share low R values. Higher R values also appears to suggest higher L2 values.
There are a few genes which have L2 values above the mean and R values below 0.1 (suggesting genes expressed highly for a small number of samples), but only a very small number. In fact I think I could be safe in deleting all genes with an R value less than 0.5.




Click for larger image

Conclusions:

The mean of all standard deviations is: 1.1074, and this plot seems to bear that out. What is interesting about this one is its similarity to the previous plot. There appear to be two large groupings of genes in the dataset. Ones with high R values and ones with very low R values, and a few genes randomly dispersed between these two groups.




Click for larger image

Conclusions:

This is the most interesting plot. As I mentioned previously, the mean of the standard deviaitons is 1.1074, and the mean of the L2 norms is 208.5677. There appears to be a large clustering of genes which are highly expressed across a few experiments and have a standard deviation which falls below the mean for all genes.


Below are the histograms for the three metrics I have looked at:


Click for larger image







Click for larger image






Click for larger image






Future Course of Action: I will be posting the results of running ARACNE shortly (within a day or so).

The great christmas white-elephant exchange with my dad's family went off like an absolute dream. ( And the rest of the day was pretty damn good too )

And as the night ended, my dad drove me to meet my mom about halfway in between Sacramento & the little town she lives in - which was the old 'hand off the daughter at the end of the weekend' routine we did when I was growing up. More nostalgic than I've been in a long time on a car ride, even if we did meet at a different place and my mom was early to the pick up spot.

Today, however, there was much christmas shopping. I'm not even calling it last minute since it's the only christmas shopping I've done. It was, however, quite productive and quite pleasing to run aroudn the downtown of our little town with my mom, in the rain, checking out the shops and talking to the shop keepers and basically having ourselves a grand time.

Tomorrow we'll be visiting with one of my highschool teachers, doing a christmas lunch, and finally after almost a week I'll be flying home and bringing my mom with me. Can't wait to be back, even if this little break from los angeles life has been so good.

I'm posting. It comes with warnings though: I'm in a vaguely maudlin mood. Talking with your stepmother and somehow coming to dissect your current emotional life after four hours will do that to anyone, I think.

So rather than try to rehash all of that sticky, scritchy, and reasonably uncomfortable dissection, here is a list of good things:

• we made chicken fricasse tonight, and it was like a taste of my childhood and oh dear god how rich is that i don't even know all thrown in together. (see recipe below for details - note though, this is in NO way a healthy thing, just GOOD)


• i have new towels, because my stepmother is a towel buying addict - she heard i wanted some and rushed me over to macy's within the hour


• last night we did dinner at the family mexican restaurant for my little sister's birthday, and they had mariachi. and the food has gotten better since the last time i was there.


• in a house where everything is sweetened with diabetic-friendly sweetners, i found the real sugar. life is much better.


• i spent yesterday doing more family visiting - with grandma, and aunt, and then sister, and got immersed in their lives for a change. It was kind of awesome.

( chicken fricasse )

hi all - I'm visiting family up state for the next couple of days. The good part is that they finally liberated themselves from dial up! The bad part is that they only have the router plugged into the house computer, no wireless, and the neighborhood is a positive sink hole of any telecommunication connection. So I'll be checking in, but not actually, you know, online.

The best part is that the world refocused for me. At least at the moment, I feel like I'm letting go of a lot of the things I convince myself are terribly important, and I'm being reminded of the things that are *actually* important. If that wasn't the most annoying and slightly cloying sentence, I don't know what is.

I woke up this morning to help my little sister rewrite her paper on moral tolerance, and it was far more difficult than I expected. Do you know what moral tolerance is? If you do, tell me? She ended up writing a paper on the slippage between society and personal morals, so that tells you how much she understood it either. I'm not built for comparative morality classes.

And then I got a pedicure with my sister, and we did what ladies do during pedicures - we talked and giggled and caught up. This evening my nephew ran me to Macy's to do more last minute shopping (which is amusing because he introduced me to the death metal bands he likes on the way -- and he's become a total death metal devote in the last year, which I find kind of adorable. Yes, adorable. Even if he does own all of Cannibal Corpse's albums). My stepmom made us dinner in a single pot (her specialty, sort of), and I walked down the street to see my other nephew's house. He teaches Japanese to high school kids, and I kind of wish I had him as a Japanese teacher. He's funny, and goofy, and he loves teaching. We talked random Japanese crap until my other nephew (his brother and housemate) got home.

Tomorrow I'm off to see my aunt's (newish) house, and visit my grandma. There's a lot of family around here. They're all kind of awesome.

ETA: If you haven't read them yet (and really, why haven't you), PLEASE GO AND READ THE AWESOME that is:

cordelianne's Here for a Good Time (Not a Long Time) S/X
Because it is PERFECT Xander voice and hot and silly with zombies!

savoytruffle's Twelve Days of Porn Kirk/McKoy Star Trek Reboot
Because it is porny and hot and crazy and just lovely.... and it is only day three!

Click for larger image



Click for larger image

Link to spreadsheet of top 500 most active genes across the sample space (as determined by the l2 norm


And here are graphical plots of the heatmaps for the metagenes obtained through the NMF algorithm. I will post a list of genes for each metagene when I am finished finding the optimal dimension for NMF for this dataset. k=50 worked well for the previous dataset, but there are many more samples in this set and there appears to be a lot of overlap between genes for that value.



Click for larger image


Click for larger image