User: mafernandez

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Posts by mafernandez

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Ion Torrent data analysis with mothur?
... Does anyone know how to analyze Ion Torrent data with mothur? Are the data suitable to be analyzed with any of the other pipelines? Thanks ...
ion torrent mothur written 11 weeks ago by mafernandez0
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Comment: C: R- Kruskal-Wallis test on multiple columns at once
... Thank you very much Jean-Karim. I will try to figure out how to finish the analysis in the way I need. As you see, I am very new to R, so within your code I could understand almost everything what you've written, but I won't be able to write it not even in a million years ;-) Cheers ...
written 4 months ago by mafernandez0
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Comment: C: R- Kruskal-Wallis test on multiple columns at once
... Sounds Great! However, I still cannot see all the Kruskal-Wallis tests. If I try something similar to: KW_test<-kruskal.test(env_fact[,i], env_fact$Categorical_var) print(KW_test) I only get a p-value, that I suppose, correspond to the test carried out as a whole and not variable per v ...
written 4 months ago by mafernandez0
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Comment: C: R- Kruskal-Wallis test on multiple columns at once
... As you can presume, I am very new at programming, so I do not know how to creat a for loop with my data. Let's say, I have variables (both numerical and categorical) in columns and samples in rows. Then I have to test each numeric variable based on each categorical one with the samples as the obser ...
written 4 months ago by mafernandez0
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Comment: C: R- Kruskal-Wallis test on multiple columns at once
... Thanks Michael If you try to get all your variables at once the result may be not robust enough. However, what I want to do is to test each variable separately, so we will have one variable and 26 observations, classified by other different parameters into groups (3 or more groups, thus Kruskal-Wal ...
written 4 months ago by mafernandez0
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Comment: A: R- Kruskal-Wallis test on multiple columns at once
... Thanks, @carambakaracho Yes, I did not point out the bioinformatic point of view of the topic. I need this analysis to be carried out on a microbial ecology study to figure out what environmental factors have any influence (or not) on the community composition. I thought my doubt could be shared ...
written 4 months ago by mafernandez0
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R- Kruskal-Wallis test on multiple columns at once
... This maybe sounds a bit simple, but I cannot get the answer. I have a dataset in R that has 26 samples in rows and many variables (>20) in columns. Some of them are categorical, so what I need to do is to carry out a Kruskal Wallis test for each numerical variable depending on each categorical o ...
statistics R test kruskal-wallis r-statistics written 4 months ago by mafernandez0
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Comment: C: Error with makeblastdb from UniProt fasta file: no sequences were found
... Seems to work! Thanks a lot. I will try to continue with downstream analyses on Genome Workbench and if I have any other issue I will post it here. Cheers! ...
written 9 months ago by mafernandez0
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Comment: C: Error with makeblastdb from UniProt fasta file: no sequences were found
... Got it. I will try to do it that way. However, with this solution, I will skip the creation of my own database, won't I? So, if I have a sequence that is not in NCBI databases (or at least not so similar) I will lose the BLAST query to it, am I right? I suppose this command will work also on pro ...
written 9 months ago by mafernandez0
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Comment: C: Error with makeblastdb from UniProt fasta file: no sequences were found
... Thanks genomax. I think the option you suggest is not suitable for my issue, since my problem is in creating the database itself, not in searching within it. ...
written 9 months ago by mafernandez0

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Popular Question 9 months ago, created a question with more than 1,000 views. For How to generate an ordination plot from a distance matrix in R?

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