Moderator: karl.stamm

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karl.stamm3.1k
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Posts by karl.stamm

<prev • 414 results • page 1 of 42 • next >
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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 4 days ago by karl.stamm3.1k
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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 8 days ago by karl.stamm3.1k
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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 15 days ago by karl.stamm3.1k
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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 19 days ago by karl.stamm3.1k
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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 26 days ago by karl.stamm3.1k
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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 27 days ago by karl.stamm3.1k
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Comment: C: R multiple parameters
... Oh that's really nice! ...
written 5 weeks ago by karl.stamm3.1k
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Comment: C: R multiple parameters
... This is a limitation of the way vioplot is written. I remember years ago editing its source to accept a list of vectors. Sorry I don't have it to share, I just remember there was no function you're looking for. In plain R you could have multiple single plots with par(mfrow) and a loop. Because it ac ...
written 5 weeks ago by karl.stamm3.1k
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Comment: C: Huge matrix memory issue
... R isn't anywhere near memory efficient. It's going to need more RAM than we can estimate. I suggest this task be computed as a list of genes, so each is a separate entity that does not need to be kept in memory. Call an optimized program like bedtools to calculate each row for you in one step. ...
written 6 weeks ago by karl.stamm3.1k
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Comment: C: Detecting isoforms in raw counts (or FPKM) after htseq-count
... Every row of the file is an isoform. Just open it up in Notepad and take a look. Now you've detected them! ...
written 8 weeks ago by karl.stamm3.1k

Latest awards to karl.stamm

Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 12 weeks 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
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 10 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 13 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Appreciated 13 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 15 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Appreciated 15 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 18 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 19 months ago, created a post with more than 5 votes. For C: Entropy Of Dna Sequences
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Voter 19 months ago, voted more than 100 times.
Scholar 19 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Scholar 20 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?

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