text:
# 5, Fos r= ~l+W-l evalule Zxlkxr) 7. ( F)-

###### Question:

5, Fos r= ~l+W-l evalule Zxlkxr) 7. ( F)-

#### Similar Solved Questions

##### Difference of proportions problem_ Biofeedback is treatment technique inwhich people are trained to improve their health by using signals from their own bodies_ A study was conducted to compare biofeedback treatmentfor chronic pain with an NSAID medica treatment group of 2100 newly diagnosed chronic pain patients were randomly assigned to receive one of the two treatments.After sixweeks of treatments_ the pain level of the patients was assessed and the results are shown inthe table below:Signifi
Difference of proportions problem_ Biofeedback is treatment technique inwhich people are trained to improve their health by using signals from their own bodies_ A study was conducted to compare biofeedback treatmentfor chronic pain with an NSAID medica treatment group of 2100 newly diagnosed chronic...
##### Build rational expression into an equivalent expression with the given denominator.$rac{12-h}{h^{2}-81} ; 3(h+9)(h-9)$
Build rational expression into an equivalent expression with the given denominator. $\frac{12-h}{h^{2}-81} ; 3(h+9)(h-9)$...
##### An educator wants to evaluate four different methods aimed atreducing the time children spend "off task" in the classroom. Totest these methods, she implements one method in each of foursimilar classrooms and records the time spent off task (in minutes)in each classroom. The results are given in the table.ClassroomMethodABCD640521531204455244622044121330320354(a) Complete the F-table. (Round your answers totwo decimal places.)Source ofVariationSSdfMSFBetweengroupsWithingroups (error)To
An educator wants to evaluate four different methods aimed at reducing the time children spend "off task" in the classroom. To test these methods, she implements one method in each of four similar classrooms and records the time spent off task (in minutes) in each classroom. The results ar...
15.41 Like-Kind Exchange. T transferred his farmland (100% business) to V in exchange for a parcel of unimproved urban real estate held by V as an investment. The farm was valued at $400,000 and was subject to a mortgage obligation of$260,000. T's basis in the farm was $340,000. The urban real ... 1 answer ##### The demand equation for a certain product is given by p = f(q) = 25/3q2 +2... The demand equation for a certain product is given by p = f(q) = 25/3q2 +2 where p is the unit price in dollars and q is the quantity demanded each year, measured in thousands of units. It is expected that the demand will be 2000 units for the year, with a maximum error of 10%. What is the maximum e... 1 answer ##### We were unable to transcribe this image사 3A4 3 3서 We were unable to transcribe this image사 3A4 3 3서... 1 answer ##### Arctica manufactures snowmobiles and ATVs. These products are made in different departments, and each department has... Arctica manufactures snowmobiles and ATVs. These products are made in different departments, and each department has its own manager. Each responsibility performance report only includes those costs that the particular department manager can control: raw materials, wages, supplies used, and equipmen... 5 answers ##### In exercises 1-8, find the arc length of each curve; compute one exactly and approximate the other numerically:r = sint 0 <t<7 =sinttr = Sin [ 0<I J =Isint(b) In exercises 1-8, find the arc length of each curve; compute one exactly and approximate the other numerically: r = sint 0 <t<7 =sintt r = Sin [ 0<I J =Isint (b)... 5 answers ##### Back in her younger days; Miss Kito was star softball player at Fishtopia High School. the league, 70% of the opposing pitchers were right-handed_ Each time Miss Kito faced right-handed pitcher there was 25%6 chance she would get hit (her batting average against righties was 0.250). On the other hand, Miss Kito had solid 0.340 batting average against [ left-handed pitchers:Fill in the tree diagram with the provided information. (No need to box this answer )What Miss Kito'$ overall batting
Back in her younger days; Miss Kito was star softball player at Fishtopia High School. the league, 70% of the opposing pitchers were right-handed_ Each time Miss Kito faced right-handed pitcher there was 25%6 chance she would get hit (her batting average against righties was 0.250). On the other ha...
##### And tha eigenvalues and elgenvectors e matnzKUICW sluge? If yes;diagonalizing matnrp
And tha eigenvalues and elgenvectors e matnz KUICW slug e? If yes; diagonalizing matnrp...
##### A batter hits a baseball $1 \mathrm{~m}$ above the ground toward the center field fence, which is $4 \mathrm{~m}$ high and $120 \mathrm{~m}$ from home plate. The ball leaves the bat with speed $35 \mathrm{~m} / \mathrm{s}$ at an angle $50^{\circ}$ above the horizontal. Is it a home run? (In other words, does the ball clear the fence?)
A batter hits a baseball $1 \mathrm{~m}$ above the ground toward the center field fence, which is $4 \mathrm{~m}$ high and $120 \mathrm{~m}$ from home plate. The ball leaves the bat with speed $35 \mathrm{~m} / \mathrm{s}$ at an angle $50^{\circ}$ above the horizontal. Is it a home run? (In other wo...
##### Orbital geometry and molecular shape are important concept to predict the molecular structure based on the lectron domains and VSEPR theory: ICs crucial for understanding the molecular structure of many different compounds_ To get points , you need t0 post - single post to show an analgy electron domain geometry and molecular geometry with objects the real world, and discuss the similarity of shapes of the molecules and real objects. Molecular shapes to discuss: Irigonal planar; tetrahedral, tri
Orbital geometry and molecular shape are important concept to predict the molecular structure based on the lectron domains and VSEPR theory: ICs crucial for understanding the molecular structure of many different compounds_ To get points , you need t0 post - single post to show an analgy electron do...
##### 14. You are driving an ambulance through traffic at 10 m/s to the scene of a...
14. You are driving an ambulance through traffic at 10 m/s to the scene of a vicious cheetah attack. A police car is already there. Both the ambulance and the police car have sirens that generate 800 Hz tones. When you are 1 km away, the police siren's loudness is approximately 40 dB. a. (6 poin...
##### 43, Qucatlon 003 Wite the exprossion the fomm kx" _ Give the values ol k andEnter the exact answers. Note that already provided, Do not Include this Your submited responsethis questionEdit
43, Qucatlon 003 Wite the exprossion the fomm kx" _ Give the values ol k and Enter the exact answers. Note that already provided, Do not Include this Your submited response this question Edit...
##### 9) P(X>39)= (Round to four decimal places as needed.)10) P(35<X<65)= (Round to four decimal places as needed.)11) P(57â‰¤Xâ‰¤67)=(Round to four decimal places as needed.)12) P(55<Xâ‰¤70)=(Round to four decimal places as needed.)13) Assume the random variable X is normally distributedwith mean Î¼=50and standard deviation Ïƒ=7.Find the 90th percentile.The 90th percentile is(Round to two decimal places as needed.)14) The number of chocolate chips in an 18-ounce bagof chocolate chip cook
9) P(X>39)= (Round to four decimal places as needed.) 10) P(35<X<65)= (Round to four decimal places as needed.) 11) P(57â‰¤Xâ‰¤67)= (Round to four decimal places as needed.) 12) P(55<Xâ‰¤70)= (Round to four decimal places as needed.) 13) Assume the random variable X is norm...
##### Find tan (14x + 29)d* =?Oa No correct answer 14 0b +C 1 + 29x214tan-! (14x + 29)Ink1 + 14x| + C(14x +29) tan (14x + 29) In/(14x+ 29)+1/+c 14 2829 xtan (14x + 29) 14Inf1 29x2 |+c
Find tan (14x + 29)d* =? Oa No correct answer 14 0b +C 1 + 29x2 14tan-! (14x + 29) Ink1 + 14x| + C (14x +29) tan (14x + 29) In/(14x+ 29)+1/+c 14 28 29 xtan (14x + 29) 14 Inf1 29x2 |+c...
##### Problems 1-3,draw out your answcr volume each tube label your dilution factor of each = drawing with the tube (write this below ? aliquot; starting solvent being used_ the tubes), diluent, andPerform two-fold serial dllution starting from Loding 14512 solution using distilled water Vour Serum Albumin (BSA) = solvenl: stock solutionPerform five-fold serial dilution starting from 1;25 Bovine Serum Albumin (BSA) stock solution to 143125 solution using distilled water a5 your sohvent.Perform seven
problems 1-3,draw out your answcr volume each tube label your dilution factor of each = drawing with the tube (write this below ? aliquot; starting solvent being used_ the tubes), diluent, and Perform two-fold serial dllution starting from Loding 14512 solution using distilled water Vour Serum Alb...
##### Gene regulation in eukaryotes is more complicated than bacteria" gene regulation Which of the following describes gene regulation event that occurs in eukaryotes but not in bacteria? In eukaryotes, mRNA degrades quickly compared to bacterial mRNA that is more stableIn eukaryotes, transcription and translation occur in the same cellular compartment: In eukaryotes; mRNA does not need to be modified. In eukaryotes; proteins are post-translationally modified, whereas bacterial proteins are neve
Gene regulation in eukaryotes is more complicated than bacteria" gene regulation Which of the following describes gene regulation event that occurs in eukaryotes but not in bacteria? In eukaryotes, mRNA degrades quickly compared to bacterial mRNA that is more stable In eukaryotes, transcription...
Let f(z) be the function whose graph is shown to the right: If Newton'$method were used t0 find root of f with initial approximation estimale the value of the second approximation T2. (a) 3 (b) ? (c) 2 (d) { (e) 0... 1 answer ##### Please solve ASAP BpF 2UF loy Please solve ASAP BpF 2UF loy... 1 answer ##### QUESTION 13 A company has decided to use 0-1 (binary) integer programming to help to make... QUESTION 13 A company has decided to use 0-1 (binary) integer programming to help to make some investment decisions. There are three possible investment alternatives from which to choose, but if it is decided that a particular alternative is to be selected, the entire cost of that alternative will b... 1 answer ##### Quick Producers acquired factory equipment on January 1, 2020, costing$39,000. In view of pending technolog-...
Quick Producers acquired factory equipment on January 1, 2020, costing $39,000. In view of pending technolog- ical developments, it is estimated that the machine will have a resale value upon disposal in four years of$8,000 and that disposal costs will be \$500. Data relating to the equipment follow...
##### Please show full work while solving The following compounds all display the NaCl structure. (i.e. They...
Please show full work while solving The following compounds all display the NaCl structure. (i.e. They are isomorphous.) For each pair, indicate which would have the lattice energy of lesser magnitude. ROCI OKCI Sro Mgo CBao CSF Mgo Mgs Case Cas Consider how the relative energies of interaction of &...
##### Consider the matrix transformation T:R → R given by T(x,y,z) = (x+ay, x+(a+1)y, x+ay+z) where a...
Consider the matrix transformation T:R → R given by T(x,y,z) = (x+ay, x+(a+1)y, x+ay+z) where a = 13. First use inverse of transformation to find T-(2,1,2). if T-(2,1,2)=(b,c,d) then b+c+d =...


text:
Search
Question: Using GOsemsim to calculate semantic similarity between orthologus genes of two species
0
19 months ago by
United States

Hi,

I know this question has been asked before a long time ago and I don't see an answer of that question in the mailing list or in the vignette of GOsemsim package. So I was wondering what is the easiest possible way of calculating GO semantic similarity value for orthologus gene pairs between two species using the above R package or any other package you know of. I am not doing this for less annotated species I need to calculate that for orthologus genes between Human and Mouse (both of which are well annotated IMHO). So I would much appreciate it if anyone who has already done this before can point me to a resource which already has pre-calculated semantic similarity values for Mouse and Human orthologues or has inbuilt code to do that.

Thanks & regards

modified 19 months ago by Guangchuang Yu1.0k • written 19 months ago by saadmurtazakhan10
0
19 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

This is not supported by GOSemSim, if you are talking about using geneSim/mgeneSim, which will mapped gene ID to GO terms by GOSemSimDATA object which used OrgDb object internally, and if IC methods were used, we also need to pre-calculate information content of each GO term.

Cross species semantic similarity measurement can be possible if I implement a function to merge GOSemSimDATA objects (e.g. one from human and one from mouse, the function should be chainable, so multiple objects can be merged sequentially). In this way you can use the merged object as background annotation to calculate semantic similarity among genes using geneSim/mgeneSim.

This is now on the TODO list, I may add this functionality to next release.

Currently, it is still possible if you use Wang method which don't need pre-calculated IC. You can firstly map your input genes to GO terms and use mgoSim to calculate their similarities via Wang method which only use the GO structure.

But mgoSim also takes semData as input. How do I bypass that?

> args(mgoSim)
function (GO1, GO2, semData, measure = "Wang", combine = "BMA")

1

I meant what should I specify as semData. In the vignette it uses hsGO as semdata. Since here the data is from two different species what should be semData here.

As I said, merge two semData from two different species will be in TODO.

Currently, what you can do is mgoSim(measure="Wang"). In this case, see the following example:

> d=godata(ont="MF")
> go1 <- c("GO:0004022", "GO:0004024", "GO:0004023")
> mgoSim(go1, go1, semData=d, measure="Wang", combine=NULL)
GO:0004022 GO:0004024 GO:0004023
GO:0004022      1.000      0.869      0.869
GO:0004024      0.869      1.000      0.747
GO:0004023      0.869      0.747      1.000
> mgoSim(go1, go1, semData=d, measure="Wang")
[1] 1

But in this example you still have to give semData as an argument. Should I give hsGO or mmGO as semData or would both yeild similar results?

In this case, mgoSim only need the information of which ontology is using.

using hsGO or mmGO as semData will generate identical result, since species information will not used in mgoSim(measure="Wang").

Thanks that helps.

Some of the genes where number of GO terms are not equal always return 1. Is that an accurate value for functional similarity to use? what can be possible turnaround for the same other than not considering those genes altogether?

number of go terms is not a factor in semantic similarity calculation.

So whats explains the reason for so many gene pairs having value 1?

as you are comparing orthologus genes, it is expected.

did you read the document? If you did, you may want to try 'avg' combine method.

format: plain


text:
# 15.37 Over the past 30 years, public awareness and concern about air pollution have escalated...

15.37 Over the past 30 years, public awareness and concern about air pollution have escalated dramatically. Venturi scrubbers are used for the removal of submicron particulate matter from smoke stacks. An experiment was conducted to determine the effect of air flow rate, water flow rate (liters/minute), recirculating water flow rate (liters/minute), and orifice size (mm) in the air side of the pneumatic nozzle on the performance of the scrubber, as measured by the number of transfer units. The results are stored in . Develop the most appropriate multiple regression model to predict the number of transfer units. Be sure to perform a thorough residual analysis. In addition, provide a detailed explanation of your results.

## Expert's Solution

Related Questions in Managerial Accounting - Decision Making
• DECISION SUPPORT TOOLS (Solved) May 05, 2014

that 35% of people attending the information sessions would have the surgery if she reduced the price to $1,500 per eye or$3,000 in total. Under this scenario how much revenue per week...

Solution Preview :
I had changed theory of your friends assignment completely. Only the common part now is what is specifically asked in question: Describe 3 types of heuristics developed by T&K. ONly 3...
• Managerial Accounting (Solved) December 09, 2012

on each page. Number each page. Do not include a table of contents. Clearly structure your response to correspond to the structure of the assignment (e.g., “Part C, Q. 1”). Print the word...

Solution Preview :
FMAC 503 Final Individual Assignment December 2012 Guidelines Please communicate your answer in a simple, clear way. Show all of your work in a Word document. Fit your work onto 8 ½ x 11...
• scuba (Solved) August 25, 2011

, but not profits, and adjust for the circumstances of the new shop. b.)State clearly any assumptions that you make to complete the financial statements. Ignore any foreign currency...

• 14.40 A real estate association in a suburban community would like to study... (Solved) May 13, 2015

you need to make about the slope of selling price with number of rooms? l. Add an interaction term to the model and, at the 0.05 level of significance, determine whether it makes a...

Solution Preview :
4.40 A real estate association in a suburban community would like to study the relationship between the size of a single-family house (as measured by the number of rooms) and the selling...
• 15.29 Crazy Dave has expanded his analysis, presented in Problem 14.73 on... May 13, 2015

. BB2009 Cp a. Develop the most appropriate multiple regression model to predict a team’s wins. Be sure to include a thorough residual analysis. In addition, provide a detailed...