User: NHEJ

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NHEJ320
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320
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4 years ago
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Posts by NHEJ

<prev • 34 results • page 1 of 4 • next >
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Should I use data scaling for heatmaps?
... I read this post and was still confused about how to use the scale feature of the heatmap command: https://www.biostars.org/p/15285/ For example, the following source states that scale=None is the default standard of use in the heatmap.2 command (see comments section of this link): https://biomickw ...
rna-seq heatmap written 4.1 years ago by NHEJ320 • updated 4.1 years ago by svlachavas580
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Comment: C: HeatmapGenerator: High performance RNAseq and microarray visualization software
... Mikhail, I think what you’re missing here is the point that many a wet-lab expert will not want to write or even want to understand the code snippet you wrote in #5 to make a heatmap. They’ll just give it to someone else.  Just to get your code off the ground in #5 you need to set your working direc ...
written 4.8 years ago by NHEJ320
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Answer: A: HeatmapGenerator: High performance RNAseq and microarray visualization software
... Giving wet-lab people an opportunity to make heatmaps directly in R without needing to know how to program in R is broadly useful for RNA-seq and microarray research.  I've never seen programming languages get synthesized together like that before so I googled for "hybrid computational pipeline" and ...
written 4.8 years ago by NHEJ320
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Comment: C: Can differential gene expression heatmaps be compared across multiple separate e
... I understand that even though merging is probably the safer option, is it still safe to compare separate heat maps (given that they share common replicates)? ...
written 4.8 years ago by NHEJ320
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When to use FPKM over raw counts or vice-versa?
... Similar to this question on biostars (https://www.biostars.org/p/68126/), can someone provide some insight on when using RNA-seq raw count data is advantageous over using FPKM (and vice-versa)?  Thanks! ...
fpkm counts rna-seq written 4.8 years ago by NHEJ320 • updated 4.8 years ago by Devon Ryan92k
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Can differential gene expression heatmaps be compared across multiple separate experiments?
... Can heatmaps be compared across multiple different experiments?  Obviously, you can compare sample runs within a single heatmap, but what about comparing sample runs in one heatmap to sample runs in another heatmap (e.g., if I want to track the activity of a gene across multiple therapeutic treatmen ...
rna-seq heatmap written 4.8 years ago by NHEJ320 • updated 4.8 years ago by Jason890
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Comment: C: FPKM vs raw counts vs RPKM
... By noncoding, I mean in the intronic portions of the genome, such as those that may produce lncRNAs. ...
written 4.8 years ago by NHEJ320
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Comment: C: FPKM vs raw counts vs RPKM
... Could you please explain how certain transcripts can have FPKM of 0.0000?  How does this assignment happen and how does Cufflinks calculate this estimate? ...
written 4.8 years ago by NHEJ320
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Comment: C: FPKM vs raw counts vs RPKM
... I'm also a bit confused in your explanation of splice junctions... You're saying that without splice junctions means anything that maps unspliced must be an exon.  But what if the read is from a noncoding part of the genome (this would not map to an exon but could potentially span a splice junction) ...
written 4.8 years ago by NHEJ320
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Comment: C: FPKM vs raw counts vs RPKM
... +1 for down to Earth answer.  But I don't understand your logic when you say "and that's why the reads map probabilistically (does not report read counts)."  Could you please expand on this?  Are you saying that FPKM is determined probabilisticly according to some sort of algorithm prediction which ...
written 4.8 years ago by NHEJ320

Latest awards to NHEJ

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Are exons within a .gtf file experimentally verified or computationally predicted?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Is ggplot2 better than heatmap.2 in R?
Scholar 4.8 years ago, created an answer that has been accepted. For A: HeatmapGenerator: High performance RNAseq and microarray visualization software
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Are exons within a .gtf file experimentally verified or computationally predicted?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Are exons within a .gtf file experimentally verified or computationally predicted?
Student 5.1 years ago, asked a question with at least 3 up-votes. For Drawing ChIPseq graphics
Student 5.2 years ago, asked a question with at least 3 up-votes. For Drawing ChIPseq graphics

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