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From: Laurent <lutgenl@icloud.com>
Subject: Re: Some advice required [OT]
Date: Tue, 28 Dec 2021 04:54:51 -0800 (PST)	[thread overview]
Message-ID: <f35c6d2f-c495-40ae-9f01-dfe0870ea063n@googlegroups.com> (raw)
In-Reply-To: <875d209a-9504-4cdb-86cd-ce9b220a4a92n@googlegroups.com>

On Tuesday, 28 December 2021 at 10:05:50 UTC+1, Laurent wrote:
> On Tuesday, 28 December 2021 at 08:48:32 UTC+1, Laurent wrote: 
> > On Tuesday, 28 December 2021 at 01:29:57 UTC+1, Ben Bacarisse wrote: 
> > > Laurent <lut...@icloud.com> writes: 
> > > 
> > > > On Monday, 27 December 2021 at 21:49:18 UTC+1, Ben Bacarisse wrote: 
> > > >> Laurent <lut...@icloud.com> writes: 
> > > >> 
> > > >> > On Monday, 27 December 2021 at 14:14:42 UTC+1, Ben Bacarisse wrote: 
> > > >> >> Laurent <lut...@icloud.com> writes: 
> > > >> >> 
> > > >> >> > On Monday, 27 December 2021 at 12:16:27 UTC+1, Niklas Holsti wrote: 
> > > >> >> > 
> > > >> >> >> Sorry, but I found your problem description impossible to understand. 
> > > >> >> >> Try to describe more clearly the experiment that is done, the structure 
> > > >> >> >> of the data the experiment provides (the meaning of the Excel rows and 
> > > >> >> >> columns), and the statistic you want to compute. 
> > > >> >> > 
> > > >> >> > Sorry tried to keep it short, was too short. 
> > > >> >> > 
> > > >> >> > Columns are the antimicrobial drugs 
> > > >> >> > Rows are the microorganism. 
> > > >> >> > 
> > > >> >> > So every cell contains a result of S, I, R or simply an empty cell 
> > > >> >> > 
> > > >> >> > S = Sensible 
> > > >> >> > I = Intermediate 
> > > >> >> > R = Resistant 
> > > >> >> > 
> > > >> >> > empty cell <S<I<R 
> > > >> >> > 
> > > >> >> > If a patient has 3 strains of the same microorganism but with 
> > > >> >> > different resistance profiles I have to find the most resistant 
> > > >> >> > one. Or if they are different I keep them all. 
> > > >> >> > 
> > > >> >> > I have no idea how to explain what I am doing to the compiler. 
> > > >> >> I think when you can explain it to people, you'll be able to code it. I 
> > > >> >> am still struggling to understand what you need. 
> > > >> >> > Why I would choose result from strain B over the result from strain A. 
> > > >> >> > 
> > > >> >> > strain A: SSSRSS 
> > > >> >> > strain B: SSRRRS 
> > > >> >> Let's space it out 
> > > >> >> 
> > > >> >> drug 1 drug 2 drug 3 drug 4 drug 5 drug 6 
> > > >> >> strain A S S S R S S 
> > > >> >> strain B S S R R R S 
> > > >> >> 
> > > >> >> You want to choose B because it has is resistant to more drugs, yes? 
> > > >> >> 
> > > >> > 
> > > >> > Yes indeed 
> > > >> > 
> > > >> >> I think, from the ordering you give, you need a measure that treats an R 
> > > >> >> as "more important" that any "I" which is "more important" than an "S". 
> > > >> >> (We will come to empty cells later.) 
> > > >> >> 
> > > >> >> I think you need to treat the number of Rs, Is and Ss like digits in a 
> > > >> >> number. In base 10, the strains score 
> > > >> >> 
> > > >> >> R S I 
> > > >> >> strain A 1 5 0 = 150 
> > > >> >> strain B 3 3 0 = 330 
> > > >> >> 
> > > >> >> Now, in fact, you don't need to use base 10. The smallest base you can 
> > > >> >> use is one more than the maximum number of test results. If there can 
> > > >> >> be up to 16 tests (say) the score is 
> > > >> >> 
> > > >> >> n(R)*17*17 + n(S)*17 + n(I). 
> > > >> >> 
> > > >> >> If this suits your needs, we can consider empty cells later on. It's 
> > > >> >> not at all clear to me how to compare 
> > > >> >> 
> > > >> >> strain C R____ 
> > > >> >> strain D RRSSSS 
> > > >> >> 
> > > >> >> Strain C is "less resistant" but only because there is not enough 
> > > >> >> information. In fact it seems more serious as it is resistant to all 
> > > >> >> tested drugs. 
> > > >> >> 
> > > >> > 
> > > >> > Strain C is probably garbage and I would remove it. With a bit of luck I will have the result with the same sample Id which would be complete. 
> > > >> > 
> > > >> >> And then what about 
> > > >> >> 
> > > >> >> strain D SR 
> > > >> >> strain E RS 
> > > >> >> 
> > > >> > 
> > > >> > Yes those are the cases which are annoying me. 
> > > >> > 
> > > >> > That's why I came up withe idea of multiplying the value of the result 
> > > >> > (S=1, I=2 and R=3) with the position of the value. Tried it with 
> > > >> > triplets but there will still be cases where different results will 
> > > >> > give the same numeric value. Ignoring empty cell able tps for the moment. 
> > > >> > 
> > > >> > Strain F: SSR (1*1+2*1+3*3) =12 and Strain G: RRS (1*3+ 2*3+3*1) = 12 
> > > >> > will be the same numerical value but they are different resistance 
> > > >> > profiles I would in this case keep both. 
> > > >> > 
> > > >> > How to prevent that from happening. 
> > > >> Can you first say why the suggestion I made is not helpful? 
> > > >> 
> > > >> -- 
> > > >> Ben. 
> > > > 
> > > > You mean that one: 
> > > > 
> > > >> >> I think you need to treat the number of Rs, Is and Ss like digits in a 
> > > >> >> number. In base 10, the strains score 
> > > >> >> 
> > > >> >> R S I 
> > > >> >> strain A 1 5 0 = 150 
> > > >> >> strain B 3 3 0 = 330 
> > > >> >> 
> > > > 
> > > > Different resistance profiles same result: 
> > > I don't yet understand the requirements so I am taking it in stages. 
> > > The first requirement seemed to be "more or less resistant". To do that 
> > > you can use digits in a large enough base but this will make the number 
> > > of Rs, Ss and Is paramount. Is that acceptable as a first step? 
> > > 
> > The requirements are one strain of a certain microorganism/patient 
> > The most resistant one or if they have different profiles 
> > 
> > SRS vs RRS => last one, more Rs 
> > 
> > SRS vs RSR = both, different profiles 
> > > In order to help people to be able to make further suggestions, maybe 
> > > you could give the relative ordering you would like to see between the 
> > > following sets of profiles. For example, between SSR, SRS and RSS, I 
> > > think the order you want is RSS > SRS > SSR. 
> > > 
> > > 1: SSR, SRS, RSS 
> > > 
> > > 2: RSI, RIS, SRI, SIR, IRS, ISR 
> > > 
> > > 3: SSSR, SSRS, SRSS, RSSS 
> > > 
> > > 4: RRSSS, RSSSR, RIIII, SRIII, RSIII, IIIRS, IIISR 
> > > 
> > The order of the results is given by the ID of the drug in the extraction tool. 
> > I could probably order them by family and hierarchy of potence but 
> > would that make a difference? 
> > > It's possible you could make do with an extra field (or digits) that 
> > > gives some measure of the relative ordering between otherwise similar 
> > > sequences. For example, using base 10 (for convenience of arithmetic) 
> > > both RRSSI and RSRSI would score 212xx but the last xx would reflect the 
> > > positioning of the results in the sequence. There are lots of way to do 
> > > this. One way would be use, as you were thinking, some sort of weighted 
> > > count. Using S=0, I=1 and R=2 with weights 
> > > 
> > > 54321 
> > > RRSSI scores 2*10000 + 1*1000 + 2*100 + 2*(5+4) + 0*(3+2) + 1*1 = 21219 
> > > RSRSI scores 2*10000 + 1*1000 + 2*100 + 2*(5+3) + 0*(4+2) + 1*1 = 21217 
> > > 
> > So to be sure that I am following: 
> > 
> > 2*(5+4) = value of R (=2) * position of R(@5 and @4) 
> > 2*(5+3) = value of R (=2) * position of R(@5 and @3) 
> > 
> > 0*(3+2) = value of S (=0) * position of S(@3 and @2) 
> > 0*(4+2) = value of S (=0) * position of S(@4 and @2) 
> > 
> > 1*1 = value of I (=1) * position of I (@1) 
> > 
> > 2*10000 + 1*1000 + 2*100 Is just used as padding? So 212 could be any other 
> > number? 
> >
> Eh forget the last sentence, brain fart: I have 2 R's so 2*10000, 1 I so 1*1000 and 2 S's so 2*100
> > But in this example I would have to keep both as drug 5,2 and 1 are common 
> > to both results but 4 and 3 are unique. 
> > 
> > The score would be completely misleading. 
> > 
> > So if my table has a width of 20 columns the first column would be 
> > 10^20, the next 10^19,.... +/- a few 0s off? 
> > 
> > I would have to implement it and see what I get as result. 
> > > If you absolutely must never get duplicate numbers, but you still want 
> > > to preserve a strict specified ordering, I think you will have much more 
> > > work to do. 
> > > 
> > > Getting a unique number for each case it trivial (but the ordering will 
> > > be wrong) and getting an ordering that rates every R > every S > every I 
> > > is also trivial, but there will be lots of duplicates. It's finding the 
> > > balance that's going to be hard. 
> > > 
> > > -- 
> > > Ben. 
> > I have prepared a cleaned up Excel workbook with only the duplicates which 
> > pose problems. The ones I would keep have an orange ID. 
> > I could upload it to Github. If that helps understanding the different cases. 
> > 
> > Thanks for your patience 
> > 
> > Laurent

Ben,

I have implemented your solution but I don't understand the reason why S would have a value of 0?
I then don't need to take care of the S'es because the result will always be 0. Not that it changes a lot

Because I still couldn't choose the profile of interest only based on the numbers.

R	R	S	S	I	 Ben's Solution: 212 11 Mine: 212 1205 
R	S	R	S	I	                            212 13            212 1405 
R	R	R	S	I	                            311 17            311 1805
R	S	R	R	I	                            311 21            311 1407
S	R	R	R	I		                    311 23            311 1607

311 17 and 311 23 being the most likely but unclear where the difference might be.

I have adapted my current solution to include the number of R,I,S
weight of the results: S=1, I=2, R=3
weight of the position in the triplet: 1st=1, 2nd=2, 3rd=3

ie.:  R	R	R => First triplet: 1*3+2*3+3*3 = 18 
        S	I          => Second triplet 1*1+2*2 = 05

RIS count: 311 
Append 1st triplet: 311 18 
Append 2nd triplet: 311 18 05

311 18 05 and 311 16 07  being the most likely with some clues which triplet is different.

Am I not somehow introducing a bias by multiplying the value with the position in the triplet?
And then there is still the case where SSR (1*1+2*1+3*3=12) and RRS (1*3+2*3+3*1=12)
will both resolve to the same value.

With 5 values it looks easy but with 20 I am getting headaches.

I don't even know if the triplet idea is good. Got inspired by some old microorganism identification 
cards which put 3 test results into one digit to get a more compact identification profile.

Wouldn't I need some sort of Traveling Salesman Problems algorithm to find the profile
with the highest number of resistances and the highest number of triplets with high values.

Thanks

Laurent

  reply	other threads:[~2021-12-28 12:54 UTC|newest]

Thread overview: 25+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-12-27  9:21 Some advice required [OT] Laurent
2021-12-27 11:16 ` Niklas Holsti
2021-12-27 12:29   ` Laurent
2021-12-27 13:14     ` Ben Bacarisse
2021-12-27 18:24       ` Laurent
2021-12-27 19:51         ` Dennis Lee Bieber
2021-12-27 20:49         ` Ben Bacarisse
2021-12-27 22:09           ` Laurent
2021-12-28  0:29             ` Ben Bacarisse
2021-12-28  7:48               ` Laurent
2021-12-28  9:05                 ` Laurent
2021-12-28 12:54                   ` Laurent [this message]
2021-12-28 13:57                     ` Ben Bacarisse
2021-12-28 18:19                       ` Laurent
2021-12-28 13:43                 ` Ben Bacarisse
2021-12-28 16:49                 ` Dennis Lee Bieber
2021-12-29  4:20                   ` Randy Brukardt
2021-12-27 17:41     ` Dennis Lee Bieber
2021-12-27 18:56       ` Niklas Holsti
2021-12-27 19:44         ` Laurent
2021-12-28  2:10     ` Randy Brukardt
2021-12-28  6:02       ` Laurent
2021-12-29  3:58         ` Randy Brukardt
2021-12-27 17:18 ` Simon Wright
2021-12-27 18:30   ` Laurent
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