24

This is a very subtle question and I encourage you to read the Wikipedia articles on these different subjects (t-test, chi-squared test, p-value, etc) because the authors worked hard to combat common misconceptions about these commonly used statistical tests. Here is a rather oversimplified rule-of-thumb for these different tests: t-test: Used when you are ...


10

It is correct if (and only if) albinism and Down syndrome are independent events, that is, if albino people is not more nor less likely to have Down syndrome than non albino people (and vice-versa). However, doing a quick Google search I can't find any source relating albinism and Down syndrome, and therefore independence seems a reasonable assumption ...


8

The NCBI Taxonomy statistics page displays the following information: There are currently 73540 genera, 331418 species, and 23127 taxa of higher order. Since the number of taxa decreases with the genericity of the taxon, there are probably around 20000 families, give or take a few thousand.


6

The Plant List has 642 families listed: http://www.theplantlist.org/1.1/about/#changes. For a quick comparison, Wikipedia lists 522 fish families: en.wikipedia.org/wiki/List_of_fish_families 136 mammal families: en.wikipedia.org/wiki/Mammal_classification 61 amphibian families: en.wikipedia.org/wiki/List_of_amphibians 57 reptile families: en.wikipedia.org/...


6

Remi.b's answer is great, but here's something less technical if that's what you're looking for: Genetic mutations happen ALL THE TIME. Every time a cell divides, there is an error rate of about one per billion. That's a very low error rate per division, but when you multiply it by the number of divisions, times the number of cells, times the number of ...


6

In your 5 points you basically cover several concepts of evolutionary biology. 1) The number of mutations depend on mutation rate. The mutation rate varies along genome sequences, species and individuals. According to the recent DECODE study (Kong et al., 2012) a human mother transmit on average 15 mutations to her offspring and a human father transmit on ...


6

The 2011 paper How Many Species Are There on Earth and in the Ocean? indirectly answers this question as well as any other source you'll find I imagine. It estimates how many species there are total based on the rate of discovery of higher taxa; it includes plots of number of taxa over time for the major groups of life in Figure S1. Which gives: Animalia - ...


6

I think it is Chord Diagram. you can see this for more information. "A chord diagram is a graphical method of displaying the inter-relationships between data in a matrix. The data are arranged radially around a circle with the relationships between the data points typically drawn as arcs connecting the data." based on the Wikipedia


5

(This isn't an answer, but hopefully it will help get it past the experimental design into just solving the equation.) Where did you get that α0 was not determined from their data? On p. 10 (256), they state, "The prevailing direction of effective pollen dispersal within neighbourhoods (a0) that gave the best fit of the model was 91 degrees from north (...


5

Additional Info T-test As A.Kennard said t-test is applied when the random variable is normally distributed. How to know what is normally distributed is a relevant question. Regular measures which suffer some random error of measurement are normally distributed. The mean values estimated from different samples (the experiment that generates that sample may ...


5

I don't know about other groups, but about plants, number of families depends on the system you follow. Recent version of The Plant List (1.1) estimates about 352 000 species of Angiosperms and lists over 400 families. See http://www.theplantlist.org/1.1/browse/A/ It is very good and reliable source of information. Second very good source about plant ...


5

Probability of independent events Assuming the albinism and Down syndrome are independent traits, then the probability of having both traits is the product of the probability of having each trait. For more information see wiki > probability (especially the section on independent events). Albinism and Down Syndrome If (and only if) albinism and Down ...


5

You should just have 1 chi-square test to test the hypothesis. Note that the problem is asking about F2 generation, not F1. H0 in a chi-square test is your prediction based on a model; H1 is that the real outcome differs from what is expected, so you have that a little backwards. H0 should be the expected counts knowing the initial proportions and ...


4

Usually if something is not expected to behave according to some scheme then the measured values for such a parameter are assumed to be normal. It is not just with gene expression but with all types of measurements like dimensions of an object, luminosity of an electric bulb, range of a bullet etc. In any measurement, the random error is modeled using ...


4

The authors suggest a reason in their abstract: Given the observational study designs with the inherent possibility of residual confounding and reverse causation phenomena, a cautious interpretation of the results is recommended. There are variables they haven't measured that lead to the observed patterns. A simple one is that the respondees to the ...


4

I took a class in ordination methods a few months ago and found the following books helpful in better understanding the various techniques: Multivariate Statistical Methods: A Primer by Brian Manley https://www.crcpress.com/Multivariate-Statistical-Methods-A-Primer-Fourth-Edition/Manly-Alberto/p/book/9781498728966 Correspondence Analysis in Practice by ...


3

The paper by Graczyk (2007) is probably relevant for you. It says that the Gini index is a measure of reactive selectivity of kinases, with values close to zero indicating no selectivity and values close to one indicating high selectivity, and it is created in direct parallel to the Gini index in economics, which is used to describe economic inequality. In ...


3

From personal experience, nearly all count data whether from microarray or reads from RNAseq of some kind, requires a log transformation of the counts. Usually a small fraction is added to all values before doing so to zero protect. Log2(counts + 0.5) or some such. This is independent of the treatments. If you log transform one sample, you will do the same ...


3

If the values on the branches indeed represent bootstrap supports, they indicate the percentage of times a clade has been obtained in a set of trees computed from resamplings of a starting data matrix. This is irrespective of the topology within the clade or outside it, because this is merely a count of bipartitions (a branch corresponds to a bipartition of ...


3

A good place to start would be Statistical Methods for Microarray Data Analysis. I'd also suggest papers from the labs of Terry Speed, Gary Churchill, John Quackenbush, and Gordon Smyth. Also, I found some papers that specifically reflect on your exact issue: how to apply the methods developed for DNA microarrays to analyze protein arrays. Eckel-Passow et ...


3

Preprocessing will and should always depend upon the biology that you try to answer or discover (e.g.: There might be an experimental rationale to believe that some genes behave differently in individual samples - and that different samples could possibly have different distributions.) log-transforming your data by itself is usually no problem, and hugely ...


3

"Simple" insects like fruit flies can learn to associate odors with food, e.g. see here for a pretty classic example. Drosophila even show some kind of depression which is acquired. Their sexual experiences even shape their alcohol intake. You will find similar examples for other model organisms as well. So, yes, simple animals behave differently in ...


2

Define a "Hit" (based on some cutoff- evalue, score etc) Get output in the tabular format Count number of hits per query — it is usually given in the header; if you want to look for some selected hits (based on some cutoff, then you can parse the file and find out) Example file (header): # BLASTN 2.2.27+ # Query: TCONS_00036712 gene=XLOC_017996 # Database: ...


2

Someone else can probably elaborate on how "peripheral lymphocyte culture" works, but this is what the statistical results suggest to me: The results suggested that the SCE in occupational workers was significantly higher than that in controls (11.31 vs 6.37, P < 0.001). This is a two-sample t-test. Occupational workers were pooled into one group and ...


2

I am not sure I'm answering your question but I hope this will help. There are two main models of genetic drift in biology: Moran model and Wright-Fisher model. The Wright-Fisher model implies picking $N$ beads (where $N$ is the population size) with replacement in order to form the new population. Therefore, the change in allele frequency (due to genetic ...


2

You can use ordinal multinomial regression (also known as ordered logit) if the response is ordered. These methods are basically extensions of logistic regressions, but using e.g. a cumulative logit instead of the logit. However, there are a number of different assumptions you need to consider. For instance, are you going to use a proportional-odds ...


2

The advice is to not generally use ERCC spike-ins at all because of variations introduced by pipetting at the volumes they recommend. The thread also explains how to use DESeq and EdgeR with spike-in normalisation, with the process being easier significantly with DESeq, where you can use the calcSizeFactors on a count matrix of spike-in reads alone. With ...


2

Normalization of expression data is a big topic with new methods being published regularly. When approaching something like this you generally want look at people who have done similar things to what you've done, and then once you understand why they did what they did, you can ask what you need to do to answer your questions. Always keep your biological ...


2

Disclaimed: Not really an answer, but too long for a comment If I understand you correctly, this must depend entirely on the accumulated probablity of detection over the entire detection period (the time the cameras were out). If the accumulated probability of detection across all habitat types is high (approaching 1, given that the animal is present), then ...


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