Moderator: karl.stamm

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karl.stamm3.2k
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Posts by karl.stamm

<prev • 418 results • page 1 of 42 • next >
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Comment: C: File location vs path
... What are you talking about? "The object File" is about a vague as anything can be. ...
written 5 weeks ago by karl.stamm3.2k
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Comment: C: HeLa reference fasta
... According to the most comprehensive review of the HeLa genome I've seen, it's not a small change between it and hg19. It's a completely rearranged cell line. https://www.ncbi.nlm.nih.gov/pubmed/23550136 ...
written 8 weeks ago by karl.stamm3.2k
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Comment: C: How to convince the replication in RNAseq
... You need to find out the source of the RNA. The question of biological replicates or technical replicates is very important and due to the source material. Where did the (each of six) RNA come from? Your collaborators will know if they are the same cells or different. Pearson correlation is irrele ...
written 8 weeks ago by karl.stamm3.2k
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Comment: C: To find Single Nucleotide polymorphism
... You forgot to ask a question. ...
written 12 weeks ago by karl.stamm3.2k
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Comment: C: NCBI BLAST on AWS
... I don't know a lot of python, but is there a chance "while i < num_rows + 1" is doing the < before the +1, and converting while(false+1) into an infinite loop? Anyway, why not log into the remote instance with a terminal and look at what it's doing instead of using any local python at all? ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Merging two datasets related to protiens and calculating the molec weight
... You're doing an awful lot of different thing at the same time. To be effective in problem solving we ahve to break it down to smaller tasks. Find where the problem really lies. Is this a coding/variables problem, or an algorithmic problem? R can be funny with variable scoping, so don't try to do ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Survey for VEP users
... That's a good idea. Thanks for running a survey. My usage of VEP might be unusual, and I want the team to know researchers are relying on consistent inputs and outputs. ...
written 3 months ago by karl.stamm3.2k
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Answer: A: Converting TPM to FPKM
... Any conversion will have some error to it. Theoretically, the math is a quick conversion, but realistically, both of your data sets are produced by different tools with different biases. The conversion is not going to be correct. Better to try to use both sorts of data, knowing they are simply diffe ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Why does methylation data have bimodal distribution?
... Okay, great. So what is a methylation beta value? Beta is a generic parameter that means something different in each situation, but in your case it might be a probe intensity ratio, and the bi-modal indicates "off" and "on" signals. ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Why does methylation data have bimodal distribution?
... LABEL YOUR AXES. WE CANT TELL WHAT YOURE TALKING ABOUT IF THE X AXIS IS BLANK ...
written 3 months ago by karl.stamm3.2k

Latest awards to karl.stamm

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 11 weeks ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 5 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 13 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 16 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 16 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
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Appreciated 18 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 21 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 22 months ago, created a post with more than 5 votes. For C: Entropy Of Dna Sequences
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