User: Ahill

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Ahill1.6k
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Posts by Ahill

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Comment: C: Large Multi-omics Project -- Dev Approach
... This is very good advice. Really understanding all the stakeholders, and capturing the core functional requirements (the "what") before diving too far into solution design (the "how") can be so important. The bigger the project, the more important it gets. If you haven't already done it, reading ...
written 5 weeks ago by Ahill1.6k
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Comment: C: Ask for suggestions of filtering probes in affymetrix data
... That strategy for defining 'detection' seems reasonable to me, in this dataset that does not have a Affymetrix MAS Absent/Present call. And the number of surviving genes seems reasonable given your criteria. One comment about the criteria of insisting on detection in >= 50% of the samples. You ...
written 7 weeks ago by Ahill1.6k
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Comment: C: Any adaptive permutation R packages?
... Are you looking for packages like [ImPerm][1] or [coin][2]? [1]: https://cran.r-project.org/web/packages/lmPerm/lmPerm.pdf [2]: https://cran.r-project.org/web/packages/coin/coin.pdf ...
written 9 weeks ago by Ahill1.6k
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Comment: C: Proteomics Data Analysis
... Did this data come from a publication? Is there a methods description that includes the experimental design? What was the protein measurement technology? If this is mass spec data, count might refer to number of supporting peptides or spectra...or it might not. Variability percentage might be a ...
written 10 weeks ago by Ahill1.6k
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Comment: C: convert GRCh38 FASTA .fa to .vcf
... Yes if you search in the [default 2vcf reference VCF][1] on github, those 2 markers (rs369202065 and rs199476136) are not present. The reference VCF appears to be ~4 years old (`##fileDate=20151104`, `##dbSNP_BUILD_ID=146`), so if your new raw data from Ancestry is more recent, missing rsIDs might ...
written 11 weeks ago by Ahill1.6k
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Answer: A: convert GRCh38 FASTA .fa to .vcf
... You can't convert a FASTA file like the ones you've linked to a VCF in any meaningful way. FASTA files contain sequences, but VCF format is designed to capture information about variations in sequence among individuals. Why are you trying to convert from FASTA to VCF? ...
written 11 weeks ago by Ahill1.6k
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Answer: A: How to quantify positive and negative correlated genes from gene expression data
... This question has come up before - have you taken a look at the "Similar posts" list on the right hand side of this post? Any threshold you pick will ultimately be arbitrary, but what you want to do is select a threshold that provides you an estimate and bound on the the false-positive rate (type I ...
written 12 weeks ago by Ahill1.6k
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Answer: C: True meaning of global transcriptome analysis
... I'm assuming the triplicates you mention mean that you have n=3 of each of the 4 experimental conditions, for a total of 12 samples. If you want to compare cell lines, unless infection has negligible effects, you do not want to combine infected and non-infected cells into a single group. Instead, ...
written 3 months ago by Ahill1.6k
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Comment: A: How to confirm that a sequence belongs to a specific organism
... Are any of the symbionts sequenced, such that you could subtract known symbiont sequences? [This paper][1] suggests there are some squid genomes out there, might have some ideas. [1]: https://www.ncbi.nlm.nih.gov/pubmed/30674665 ...
written 3 months ago by Ahill1.6k
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Comment: C: Subread alignment issue
... What operating system are you on? Did you install from a precompiled binary matched to your OS, or from from source? Have you tried posting to the support site or user group linked from the [subread home page][1]? Those contacts might be best source of help for a malloc error like this one. [ ...
written 5 months ago by Ahill1.6k

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