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SvenKB
@SvenKB
But it returns "NULL"
Maybe anyone has the same problem or is able to help? Zoom-Room 2 here!
Leo Lahti
@antagomir
What do you have in "tse"? Can you copypaste out print(tse)
I will come soon..
SvenKB
@SvenKB
class: TreeSummarizedExperiment
dim: 151 27
metadata(0):
assays(2): counts relabundance
rownames(151): 1726470 1726471 ... 17264756 17264757
rowData names(6): Kingdom Phylum ... Family Genus
colnames: NULL
colData names(4): patient_status cohort patient_status_vs_cohort sample_name
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowLinks: a LinkDataFrame (151 rows)
rowTree: 1 phylo tree(s) (151 leaves)
colLinks: NULL
colTree: NULL
Leo Lahti
@antagomir
Ok, at least tse is not empty and it has data.
What says: assays(tse)
SvenKB
@SvenKB
List of length 2
names(2): counts relabundance
without the "order_by_sample" argument, it works. Maybe that is important to know
Leo Lahti
@antagomir
moment, I try myself
Leo Lahti
@antagomir
This is a strange issue, we need to investigate in more detail and will try to solve during this afternoon so you should be use it tomorrow at least.
SvenKB
@SvenKB
Alright, thank you!
Lena Sophie Koch
@LenaSophieKoch_twitter
I have a problem with importing data. This is what I put:
biom_file_path <- "C:\users\KochLS\Desktop\R_Workshop_Day1\table-with-taxonomy.biom"
sample_meta_file_path <- "C:\Users\KochLS\Desktop\R_Workshop_Day1\WesternDietSert_extendedTimeComparisonsv4"
tree_file_path <- "C:\users\KochLS\Desktop\R_Workshop_Day1\tree.nwk"
Gives this error
Error: unexpected symbol in "biom_file_path <- C:\users"
Tuomas Borman
@tvborm
Windows has those slash symbols in "wrong" way, try to convert \ to /
Leo Lahti
@antagomir
or try with double slash after C ie. "//" or "\"
Lena Sophie Koch
@LenaSophieKoch_twitter
ok now I did not get the error. I have the 3 files now as "Values"on the right. But I cannot click on them or view them
but I will go through the tutorial and see what's to do
Leo Lahti
@antagomir
i think they are not vieweable files but the import biom examples from section 1.3.1.1 should work
Lena Sophie Koch
@LenaSophieKoch_twitter
Yes, the following steps work :) Thanks!
Isabella Wagner
@isabellawagnr_twitter
could you please also post the solutions for section 6.3 ["Exercises (optional)" ] for both datasets 1 (ADHD) & 2 (SERT)?
3 replies
andrea_alvarez_sala
@andrea_alvarez_sala:matrix.org
[m]
Hi, I still have problems with installing the Bioc packages ("ANCOMBC", "DESeq2", "DirichletMultinomial", "mia", "miaViz"). I use windows.. Could you give me some advice? Thank you
Leo Lahti
@antagomir_gitlab
Can you print here the output of sessionInfo() in R
And then the error message that you get with mia
andrea_alvarez_sala
@andrea_alvarez_sala:matrix.org
[m]
Yes, of course
Leo Lahti
@antagomir_gitlab
I am still missing the output of sessionInfo() ...
Leo Lahti
@antagomir_gitlab
But because the error says that mia is not available for this version of R, I suspect that your R version is less than the required R-4.1.0 which was mentioned in the advance preparation instructions.
Ideally, you would install R-4.1.0. Then this should work. If this feels like too much, we could see what to do but things may be difficult, not just because of us but because these tools depend on other Independent tools in the broader R ecosystem that also rely on new R versions and are out of our control
Corinna Schulz
@Cor_Et_Cerebrum_twitter
image.png
2 replies
I had troubles converting the se to a TSE, the screenshot is above. Any ideas, why this might be the case? Thanks!
Carmen Schiweck
@carmensch:matrix.org
[m]
For the SERT dataset, would you calculate the abundances/make the table etc. seperately for each timepoint ( so subset the TSE in 2 seperate ones?)
Mirjam Bloemendaal
@mirjam_bloem_twitter
you could subset only timepoint 2
or create delta values looking at the change between t2 versus t1, but this is a bit more complex to do quickly
Lena Sophie Koch
@LenaSophieKoch_twitter

I have this error and I'm not sure how to solve it

sample_meta <- DataFrame(read.table(sample_meta_file_path, sep = ",", header = FALSE))
Warning in file(file, "rt") :
cannot open file 'C:/Users/KochLS/Desktop/R_Workshop_Day1/WesternDietSert_extendedTimeComparisonsv4': No such file or directory
Error in file(file, "rt") : cannot open the connection

1 reply
the file is where the path says
Lena Sophie Koch
@LenaSophieKoch_twitter
We figured it out!
Carmen Schiweck
@carmensch:matrix.org
[m]
I created two abundance plots, one for timepoint one and one for timepoint 2, but the color coding is changing. How can I maintain the colour code for bacteria between both timepoints?:)
2 replies
Evelyn Medawar
@evelynmedawar

wondering about dataformats that are required for mia, e.g. in estimateDiversity -> in the workbook in 7.2. > Takes subset of colData. Takes only ADHD samples
ADHD_shannon <- colData(tse)[ colData(tse)[, "patient_status"] == "ADHD" , ]

-> Takes subset of colData. Takes only samples that are in cohort 2 or cohort 3.
ADHD_shannon <- ADHD_shannon[ ADHD_shannon[, "cohort"] %in% c("Cohort_2", "Cohort_3") , ]

6 replies
then i would like to apply estimateDiversity on it, like this --> ADHD_shannon <- estimateDiversity(ADHD_shannon, index = indices, name = names)
but this won't work
Michael J.
@MADscientist314
hey is there a docker container for mia/miaviz?
Leo Lahti
@antagomir_gitlab
Hmm no.. not at the moment. But we are welcoming contributions..
Michael J.
@MADscientist314
cool! I ended up having such a dependency nightmare situation on my rstudio server that I ended up just pulling from rocker/tidyverse:4.1.0 and installing mia / miaviz from there. I can try and make the the docker file and will make a pull request to the github, as well as host the docker container directly on docker hub when I get a chance
Leo Lahti
@antagomir_gitlab
Would be great! I know docker of course but not familiar with all the current best practices etc in maintaining this way. If you do, that's excellent. We will certainly see how to best incorporate this in the other material, and all contributions are acknowledged appropriately.
Will require active maintenance atm because the miaverse is developing rapidly.
Michael J.
@MADscientist314
@antagomir_gitlab ok so I built the container off of the bioconductor base image, installed mia and miaViz, and published it on docker hub docker hub , linking the dockerfile to my github. Here is the Dockerfile that I made and built for the container ( I tried making a pull request based on the fork, but it was closed because the mia repo need to be exclusive to R stuff only).
Leo Lahti
@antagomir_gitlab
Hi! As you maybe saw now, I proposed that we create another repository for this, and if you could add some basic instructions on the requirements and how to use this would be great. The instructions could be in the repository README, or another set of md files or repository wiki, if they do not fit in the README. We could then refer to this also in the online manual.