User: O.rka

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O.rka40
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Posts by O.rka

<prev • 53 results • page 1 of 6 • next >
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Comment: A: Which method is good for getting logFC for pairwise comparsion of replicates?
... Any progress on this? I'm running the metrics on a bunch of distances measures right now to see the best one for my data set. ...
written 12 days ago by O.rka40
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Find list, flatfiles, or database of all gram + or - bacteria?
... I have an OTU table and I want to see all of the gram - and gram + bacteria in the communities. Is there a list that has all of the gram + or gram - bacteria anywhere? Preferably the genera and whether or not they are gram + or - in a table format. I am comfortable webscraping if there is a resour ...
taxonomy written 7 weeks ago by O.rka40
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Comment: C: How to merge quality trimmed interlaced reads?
... Thank you. I think I may have had some fundamental information incorrect about paired end sequencing technology. I was under the impression that you have overlapped segments so if you had 75 bp reads you would end up with ~150 bp reads. It seems like that is not the case. So for paired end reads ...
written 7 weeks ago by O.rka40
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How to merge quality trimmed interlaced reads?
... I have paired end reads from Illumina NextSeq. I've removed adapters/primers, quality trimmed, and interlaced the forward and reverse reads. I now have a single fasta (not fastq) file with the following structure: >NS500647:208:HYKFFBGX2:1:11101:9580:1154 1:N:0:GATCAG GTGGTCAGCAGACGT ...
rna-seq written 8 weeks ago by O.rka40
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What is the minimum number of non-ribosomal reads that can be used for E. coli transcriptomics?
... I have paired end Illumina NEXTSeq reads with 75 bp read-length with samples in ~triplicates (sometimes duplicates, sometimes I'll have 6). I was thinking 2 Million reads would be a good target and if there are a few replicates with high pearson correlation that have over 1 Million then that should ...
rna-seq written 8 weeks ago by O.rka40
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Is logFC in edgeR base e, 2, or 10?
... I am trying to find in the documentation of edgeR where it says the default base of the log function. I've used `exactTest` and `topTags` it gives me `logFC` but is it base `e`, `2`, or `10`? ...
differential bioconductor logfc edger written 9 weeks ago by O.rka40 • updated 9 weeks ago by Devon Ryan79k
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... Interesting answers. I will take a look at the regression. However, at that point it wouldn't be correlation values? Also, if you get some extra time can you take a look at this question about `modulePreservation` https://support.bioconductor.org/p/106661/ ...
written 10 weeks ago by O.rka40
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... Thanks for being helpful with all of those questions. I still need to look more into the details but it's a tool that I didn't even know existed. Really inspiring. ...
written 10 weeks ago by O.rka40
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... I'm getting values for this but I don't know if it makes sense since we wouldn't necessarily expect there to be a linear correlation between a continuous variable and a categorical variable right? ...
written 11 weeks ago by O.rka40
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Comment: C: How to compare 2 separate coexpression networks each with the same genes?
... If you have code snippets that can illustrate how to correlated the eigengenes with categorical data like treatment that would be very useful. I'm doing most of the computation outside of R in Python so a good understanding of the methods is crucial. For example, if I have continuous data then I j ...
written 11 weeks ago by O.rka40

Latest awards to O.rka

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 5 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 13 months ago, voted at least 25 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 21 months ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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