Monthly Archives: January 2013

edgeR: spotty documentation

Ok, just a quick post here to verbalize something that bothers me (and everybody else, I suspect).. The issue of poor documentation of software.. Even ‘well’ documented programs have huge issues.. For instance, I am working with edgeR a lot lately.. The documentation is pretty good (link), but there is a lot still left up to the investigators imagination.. For instance, when using the fiunction ‘calcNormFactors’, this is what the manual says:

Description: Calculate normalization factors to scale the raw library sizes.

Usage

calcNormFactors(object, method=c(“TMM”,”RLE”,”upperquartile”), refColumn = NULL,logratioTrim = .3, sumTrim = 0.05, doWeighting=TRUE, Acutoff=-1e10, p=0.75)

Arguments:
object: either a matrix of raw (read) counts or a DGEList object
method: method to use to calculate the scale factors
refColumn: column to use as reference for method=”TMM”
logratioTrim: amount of trim to use on log-ratios (“M” values) for method=”TMM”
sumTrim: amount of trim to use on the combined absolute levels (“A” values) for method=”TMM”
doWeighting: logical, whether to compute (asymptotic binomial precision) weights for method=”TMM”
Acutoff: cutoff on “A” values to use before trimming for method=”TMM”
p: percentile (between 0 and 1) of the counts that is aligned when method=”upperquartile”

Details
method=”TMM” is the weighted trimmed mean of M-values (to the reference) proposed by
Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data.
If refColumn is unspecified, the library whose upper quartile is closest to the mean upper quartile
is used.

Where do the default values for logratioTrim, sumTrim, etc. come from.. Should I change them? To what, how, why, when.. It would be really nice to have some guidance about when to consider changing these, and how to reasonably do so..

Of note, nearly every one of the functions contain poorly documented options, and edgeR is one of  the most well documented packages out there..

end rant..

Day 2: Field work continues

photo (2)A mostly frustrating day in the field:  I had more success in the mouse department, but they were VERY cold, and they didn’t want to eat/drink.. this part of the plan was critical.. Sleep– yes, eat, not so much..  To make sure the mice dont get so cold tonight, I bought some pillow stuffing, and filled the trap with plenty.. Hopefully tomorrow I’ll find nice, toasty mice, just waiting to drink the fresh water I’ll provide!  I also added a bit more food, hoping that some more carbs will keep their little mouse metabolism high.  Here I am holding a mouse in each hand, trying to warm them up.

_MDM0164

On my return to the station, I found my wife and kids doctoring a bat.. a western pipistrelle, which is the most common bat here in Deep Canyon.. They found it in the pool, hanging on for dear life. This poor guy must have swooped just a bit too low. He was cold, and had a torn wing. We turned him over to the reserve biologist for rehabilitation..

 

In general, the field is a great place to take the kids. Around every corner is an adventure.. a learning experience. This time of year is relatively safe (no venomous snakes), so the worst that can probably happen is getting ‘bit’ by a cactus, or a scraped knee, but finding old bones, looking through scat, digging up an ant hill, etc far outweigh this. Our kids have largely grown up as city kids, so getting them out into nature is great!

 

Update from the field

We drove a long 9 hour drive on Wednesday, through the LA basin, then east to the Inland Empire– the Southern California Deserts. As I mentioned in the last post, I am really excited for this trip, as I am collecting a bunch of interesting and important data.

I have been watching the weather, and it has been cold and dry, exceptionally so on both accounts. Neither of these factors bode well, nor does the fact that is it a moonless night. Because we ended up arriving somewhat later than expected, I set traps in the dark, using my headlamp.. this makes is difficult to optimize trap placement..

This morning, nothing… no mice, completely empty.. This is the 1st time this has happened in an extremely long time. Bummer! I decided to try my luck elsewhere, and move my traps to a new area. Thankfully, I work in a canyon where good rodent habitat is nearly contiguous. I moved over an arroyo, to a rock face that had plenty of fresh looking rodent signs.. We’ll see what heppens tomorrow.

In the absence of mice, I decided to take the family on a long walk back into the canyon. This was great, and exhausting. Several close calls with the cholla cactus, and one more serious ‘interaction’ that required I use the needle-nose pliers to remove cactus spines.  All this with 3 year old on my shoulders for much of the walk back home..

bug  In ending, we saw a cool bug. Anyone know what it is (I don’t)?