User: arf1389

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arf138910
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Posts by arf1389

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Answer: A: How should effective lengths returned by Salmon be collapsed for Differential Ex
... The answer is to this question is a feature that was added as of Salmon v 0.9.0. > Added the quantmerge command. This allows producing a multi-sample TSV > file with aggregated abundance metrics over samples from many > different quantification runs This can be used to merge technical re ...
written 15 months ago by arf138910
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How should effective lengths returned by Salmon be collapsed for Differential Expression?
... Hi All, I used [Salmon][1] to align a set of technical replicate fasta files to my reference transcriptome with the seq-bias and gc-bias corrections enabled. I know that the [tximport package][2] reports the effective length vector should be processed the following way for use in edgeR: cts & ...
alignment salmon rna-seq written 15 months ago by arf138910
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Comment: C: Can I consolidate normalized log2 biological replicates by taking mean?
... Hello arf1389! We believe that this post does not fit the main topic of this site. got the solution. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll ...
written 15 months ago by arf138910
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Comment: C: Can I consolidate normalized log2 biological replicates by taking mean?
... Doh! I just realized that since I am getting my counts returned from the random effects part of my mixed model...I can change my pedigree covariance matrix to be at the family level instead of biological. So whereas previously using the R function mmer2 from the sommer package I was running: mme ...
written 15 months ago by arf138910
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Comment: C: Can I consolidate normalized log2 biological replicates by taking mean?
... *May* be more powerful in helping to identify family transcript levels which impact a continuous phenotype. My phenotypes are on a family basis and so I'd like to consolidate the biological replicates to build a model and make predictions. Technical variation was removed by log-transforming the t ...
written 15 months ago by arf138910
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(Closed) Can I consolidate normalized log2 biological replicates by taking mean?
... If counts are normalized and log-transformed so that they have roughly a "normal" distribution, can I take the mean of biological replicates to consolidate them to a family average? I know that log transformation of numbers are not additive so that: log2(*raw_count*) = 2^(*log2*) However given tha ...
rna-seq written 15 months ago by arf138910
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How to filter normalized RNA-Seq transcripts for the purpose of predicting a continuous phenotype
... Hi All, I am looking for some help with understanding the most logical way (mathematically speaking) that I can reduce post-normalized rna-seq counts in order to fit varying regression/tree-based models for the purpose of phenotype prediction. Background: - 60 "treatments": A treatment in this ...
filtering reads rna-seq written 15 months ago by arf138910

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Scholar 15 months ago, created an answer that has been accepted. For A: How should effective lengths returned by Salmon be collapsed for Differential Ex

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