User: Ark

gravatar for Ark
Ark60
Reputation:
60
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Location:
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1 day, 5 hours ago
Joined:
4 months, 3 weeks ago
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Undergraduate bioinformatics student.

Posts by Ark

<prev • 15 results • page 1 of 2 • next >
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Comment: C: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Thanks for the link! This looks interesting and I will definitely try it out on my data! ...
written 29 days ago by Ark60
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Comment: C: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Yes, thank you. That was basically what I assumed my issue was. The solution they proposed for using a different algorithm was not applicable in my case. Also, I do actually want an extreme number of clusters, as I am running some tests that need both very low and very high numbers of clusters. Tha ...
written 29 days ago by Ark60
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Answer: A: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... I have been working with this some more and have come to the conclusion that this particular warning is practically unavoidable when I push the number of clusters as high as I am. From what I have read, with an extreme number of clusters and very similar values among the data (many practically equiv ...
written 4 weeks ago by Ark60
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K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Hello! I am attempting to run the default kmeans function in RStudio on TPM-normalized and feature-scaled RNA-seq data. I am varying the number of centers I present to kmeans (logarithmically increasing 'k' from 1 - 10,000) but I have hit a snag. I am calling the kmeans function in the following w ...
R kmeans rna-seq written 5 weeks ago by Ark60 • updated 4 weeks ago by Chirag Parsania1.2k
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Answer: A: How to "Randomly" Select Genes
... I ran into a problem with both of these methods when you have many clusters, so I wanted to post my fix here just in case anyone finds this thread later. If you have many clusters, it is likely that you will have clusters of the same size. The above methods will group together everything with the s ...
written 7 weeks ago by Ark60
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... I see, that is definitely a better approach than I am currently using. Thanks for the suggestions and the links! ...
written 9 weeks ago by Ark60
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Comment: C: How to "Randomly" Select Genes
... This is nice also. Looks a bit cleaner. Thanks! ...
written 10 weeks ago by Ark60
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... Thanks for your response Igor! I had not seen that page. Thank you for the link! I will dig through and try to determine which labels are useful for me. Do you have any recommendations on a better way to separate the protein coding genes? I am working in R and currently I am using awk and some reg ...
written 10 weeks ago by Ark60
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Finding Only Protein Coding Genes from Gencode GTF
... Hello! I am trying to filter out only the protein coding genes from the gencode gtf file found here: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.basic.annotation.gtf.gz I have found a discrepancy in the way some of the genes are labeled and it has been causing me ...
R rna-seq written 10 weeks ago by Ark60 • updated 10 weeks ago by igor7.1k
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Comment: C: How to "Randomly" Select Genes
... I see, that's interesting. Earlier in my project I created an "elbow-graph" from the WSS values to attempt to gain some insight on the number of clusters I should use. It was not as helpful as I was hoping for, but I only tried it on my data, not with any "synthetic" data to compare it to. I haven't ...
written 12 weeks ago by Ark60

Latest awards to Ark

Scholar 18 days ago, created an answer that has been accepted. For A: grep whole sequences containing a specific motif in a fasta file
Supporter 5 weeks ago, voted at least 25 times.
Scholar 12 weeks ago, created an answer that has been accepted. For A: grep whole sequences containing a specific motif in a fasta file
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: grep whole sequences containing a specific motif in a fasta file

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