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@@tehatutty yes

Column type change to group?

We wrap them in aluminium foil and then autoclave them. Ensure they are dry before using them.

Thanks for the reply! Do you wrap the whole petri dish or just the filter papers?@@LeeChoonWeng

@@MichelleMunguia-figueroa wrap the filter papers. When need, aseptically use cleaned forceps to pick the filter and place them on top of filter base

From USA

Ok

Simper usually done after Anosim if significant. For Anosim, i isually use ratio or count data. Although Anosim ranks the data, i don’t think ordinal data is suitable as its distance is not comparable

​@@LeeChoonWeng Thank you so much for the reply! Very interesting.

Did you set your first column to groups?

What type of data used? If counts usually bray curtis. If proportion maybe try cosine index

@@LeeChoonWeng Yes, bray curtis i found it. Thanks a lot.

Which tests?

@@LeeChoonWeng I want to do species refraction curve plot and similarly index for three season i. e. for summer, rainy and winter data

Can I have your gmail I have query regarding PAST

@@basudevbacha4457 leechoonweng@gmail.com

??

@@LeeChoonWeng its microbiology questions

@@LeeChoonWeng can u plz help me

@@Ilemaurice687what kind of help?

@@LeeChoonWeng can u help me in these questions Plz can u help me Q1 Determine the value of microorganisms and describe their role in different industries and/or as pathogens 2.Explain different methods of sterilization and disinfection and their mechanism of action 3. explain how microbial diversity may be determined relate the structures and functions of marine microorganisms to their habitats 4 describe the metabolic pathways in major primary producers in the marine environment 5 identify the classes of metabolic types present in various marine habitats relate microbial processes to global processes and to climate change 6 describe the various adaptations that have evolved in marine microorganisms relate these adaptations to the microenvironment design strategies to apply such adaptations in biotechnology

Try a matrix plot with column labels

Column is time

Sorry but I dont have it

I use it in my research. Published, no problems. Most important is to use the right test, and to interpret the results correctly

If in simper, and you pool your groups, the default index used is bray Curtis and cannot be changed. Therefore it will not allow recompute.

Sorry but I couldn’t access your earlier question

Glad it helped

Sorry for the late reply. File is saved as .dat file

Although you cannot double click on the file to open it, you can open from inside the PAST software

@@LeeChoonWeng Thank you. It's well solved.

Sorry for the late reply. You may save your file as a dat file. For results of analysis, I usually copy and paste into excel. For graphs, you may export as svg or png files

Anything above 50% should be worth discussing but the shape of your tree will also have to make sense.

You are welcome

Tq. Glad it’s helpful

BAM website has mpn tables. www.fda.gov/food/laboratory-methods-food/bacteriological-analytical-manual-bam

Any reason why?

@@LeeChoonWeng wanted to read the paper so as to cite the sources

@@akshayasrini6542 Lim JH, Lee CW (2017). Effects of eutrophication on diatom abundance, biovolume and diversity in tropical coastal waters. Environmental Monitoring and Assessment 189: 432

Hope this helps

@@LeeChoonWeng Thanks a lot!

Log transformed data uses paretric stats e.g. ANOVA and tukey's test. If not transformed, and if data does not fit normal distribution, use kruskal Wallis test. If p<0.05, then Mann Whitney pairwise

Parametric

OK, thank you for replying promptly. I got that. Is it the log-transformed data that I perform the parametric tests on?

@@stellauwom1710 yes

@@LeeChoonWeng thank you very much

The title of the column should follow your require ments. However PAST does not support graphical editing, and does not support spaces in column title. What I usually do is get the clearest column title possible before pasting

I hope this answers your question.

Worst case scenario is to export the graph as SVG, and use inkscape to edit the graph

www.fda.gov/food/laboratory-methods-foods/bam-chapter-3-aerobic-plate-count

If you are familiar with R, go for it. It is worth learning R. However if you are just looking for a quick and easy solution, PAST is good. Sorry but I am not familiar with maximum entropy.

@@LeeChoonWeng Thank you. And what version is your PAST program?

@@desiekaputriempra27564.03

@@LeeChoonWeng thank you so much

@@desiekaputriempra2756 no problems. Good luck

Glad the video helped

Missing face to face teaching

Great. Good luck.

@@LeeChoonWeng I LOVED YOUR TEACHING TOO.THANK YOU VERY MUCH FOR THE FUTURE I HAVE SOME QUESTION WHAT I WILL ASK YOU

Yes. Apparently when I tried with one row, an error message popped up 'requiring two rows per group'.

@@LeeChoonWeng I only surveyed the islands (group) A and B once and divided their abundance into 2 rows so each island (group) has 2 rows. PAST was able to analyzed it. I also tried putting the second rows of each island (group) as 0 abundance, PAST was able to analyzed it too but a totally different result that doesn't reflect the abundance table was produced. I believe the 1st method like the one you did in the video is correct.

@@syunsn7230 I remembered you said you measured 5 islands. I will probably calculate the alpha and beta diversities. Then use cluster analysis to check for similarities with Bray Curtis coefficient.

@@LeeChoonWeng Those 5 islands are from a different set of locations. Yes, I've calculated the diversity indices at every site and had run the cluster analysis, but it was Jaccard instead of Bray Curtis. I will run Bray Curtis too. Thank you for your input.

@@syunsn7230 Good luck

Sorry but count data would probably not fit the criteria of ANOVA (parametric stats). If you wish to test if the community profile differs among the islands, try ANOSIM (analysis of similarities).

@@LeeChoonWeng Thank you so much for your input, I shall consider ANOSIM. Btw, I ran Normality test on the abundance data on each island and Shapiro Wilk are below 0.05 for all islands. I read that Mann Whitney U test is recommended for non-normally distributed data which is similar to ANOVA. Should I report Mann Whitney U results? Some pairs of island are significantly different according to Mann Whitney U.

@@syunsn7230 since p<0.05 in Shapiro, your data do not follow normal distribution. You may report kruskal Wallis for anova, and Mann whitney pair wise for post hoc.

@@LeeChoonWeng Thank you so much for your input. I've run Kruskal Wallis in PAST and the P is 0.15. No significant difference between sample medians. However, when I checked the Mann Whitney pairwise tab next to it, 2 pairs are highlighted with significant difference with P<0.05. The results are contradicting, how do I report this?

@@syunsn7230 Mann whitney is post hoc test only if kruskal Wallis is significant. Therefore only kruskal Wallis need to be reported

Glad to hear that!

Not sure but maybe nmds to see which factor is important for the distribution of your data

Good question. The chemicals are added to the soil, and must be mixed properly. If not mixed properly, microbial growth will be in patches. The chemicals added are to see what kind of chemolithotrophy is occurring. So one has CaSO4 and the other has FeSO4. This is the main difference.

That is a very good question. I looked it up, and it is not really explained anywhere. For me, the middle set best represents the average concentration for the group.

@@LeeChoonWeng thnks for the reply. Can i have another question. If for example im looking for the fecal coliforms.that means i have to run the presumptive test first which uses lauryl tryptose broth. Then proceed to EC medium for fecal coliforms. If i get 5-5-5-0-0 result for the presumptive. So i will plant the first 3 tubes to the EC medium and get 5-5-5 as the EC medium result. The question is, should i include the first 0 in the presumptive to get a 5-5-0 result. Because 5-5-5 fecal result doest give justice to the the decrese in number of bacteria in the presumptive. TIA 😊

@@rbb6194 From your first set of results, 5-5-5-0-0, I would have chosen 5-0-0 for the EC medium. The first rule for MPN is to choose the highest dilution with all positive tubes and the subsequent two dilutions.

Version 3

@@LeeChoonWeng Thanks! Very helpful video

@@robson86 Glad it helped

@@LeeChoonWeng yeah, I just realized that ANOVA 2 way is a better way to analize my data instead of one way

@@robson86 Great!!!