User: daattali

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daattali40
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Posts by daattali

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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... There are multiple samples form each transcript (coming from multiple people) However, the number of samples per tissue is not consistent. For example, there are over 300 samples from brain, but 50-100 for most other tissues. So does the tool you mentioned help with this? ...
written 6.1 years ago by daattali40
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... Sort of :) Let's say this is my data (column names are transcripts, row names are tissue types): | A | B | C | brain | 10 | 5 | 1 | liver | 20 | 10 | 2 | lung | 5 | 2 | 0.4 | kidney | 30 | 3 | 3.5 I'll defi ...
written 6.1 years ago by daattali40
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... I initially thought about also making the variances match, but I came to the conclusion that doing that will be destructive since I want to try to find differences in the variation across tissues. I could try it though, and see what it gives me ...
written 6.1 years ago by daattali40
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... Ah, sorry for misunderstanding. The effect you're describing is also very apparent in the data though - for every protein I can clearly see that there are tissues where all the transcripts are expressed fairly high, whereas there are other tissues where all the transcripts have a proportionally lowe ...
written 6.1 years ago by daattali40
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... You are correct in that almost all the transcripts I'm looking at (for each given protein) have very different expression levels. For example: transcript A could have an average RPKM value of 4, while transcript B would have an average RPKM of 0.7, but they could have the same "pattern" across tiss ...
written 6.1 years ago by daattali40
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Comment: C: How To Find Differentially Expressed Transcripts Across Tissues?
... To simplify matters, I would just define the expression of the "reference" transcript as the "pattern" to compare other transcripts against. I realize that this is not perfect, but I figure it's a fair enough starting point. So, given the expression of the reference transcript, which transcripts var ...
written 6.1 years ago by daattali40
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How To Find Differentially Expressed Transcripts Across Tissues?
... Hello fellow bioinformaticians, This may well be an easy and solved problem, but I didn't find a standard solution for this. I'm also extremely new to the field, so please excuse me :) I have expression data for different transcripts from 386 proteins in 25 different tissues (from GTEx - yes, the ...
differential-expression rna-seq written 6.1 years ago by daattali40 • updated 6.1 years ago by lkmklsmn920
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Comment: C: Genome Compression: Why Not Just Use 7Z On Stripped Vcf?
... That makes sense, I didn't know that random access is such a high priority. Thanks. ...
written 6.2 years ago by daattali40
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Genome Compression: Why Not Just Use 7Z On Stripped Vcf?
... Hi, I'm new to genome compression, and I was reading through this recent paper and some of their results left me with an unanswered question (paper available here) In Table 5, they show that by simply stripping away all non-essential fields of a VCF file and then compressing it with 7z, it achieve ...
written 6.2 years ago by daattali40 • updated 6.2 years ago by Pierre Lindenbaum124k

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Popular Question 6.1 years ago, created a question with more than 1,000 views. For How To Find Differentially Expressed Transcripts Across Tissues?
Student 6.1 years ago, asked a question with at least 3 up-votes. For How To Find Differentially Expressed Transcripts Across Tissues?

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