User: Ahill

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Ahill1.4k
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Posts by Ahill

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Comment: C: How to demultiplex Miseq undetermined files?
... The Undetermined .fastq files contain reads where the demultiplexer can't match a barcode in your Samplesheet.csv - so those reads can't be demultiplexed. Might depend on your workflow or application, but the indexes found by the demultiplexer are typically reported in the .fastq headers, and can b ...
written 4 days ago by Ahill1.4k
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Comment: C: Interpretation of linear modelling quality test
... Following on this comment, I see the author of limma has commented about VOOM for spectral count data on Bioconductor [here][1]. For TMT data, related Bioconductor discussion [here][2]. Sebastian, worth a read if you've not already reviewed. [1]: https://support.bioconductor.org/p/64484/ [ ...
written 12 days ago by Ahill1.4k
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Comment: C: What does LnP(D) per clusters K plot means?
... FWIW, I'd start with the methods description and references in the paper where you found this figure. A google search using the y-axis title leads to [STRUCTURE][1] and associated references, and suggests LnP(D) is the natural log posterior probability of the data, conditioned on K, the number of f ...
written 16 days ago by Ahill1.4k
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Answer: A: How can multiarray results have more than 1 gene name for each row?
... The triple slash notation is used by Affymetrix annotation files for probesets that map to multiple gene identifiers. The paper likely used those annotation files as a source of gene mappings. See [here][1]: > Each row after the first row contains annotations for a single probe > set. All a ...
written 20 days ago by Ahill1.4k
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Comment: C: Good tutorials for biomarker identification for biologists familliar with R?
... Have you looked at the tutorials on this site (e.g [here][1]). [Bioconductor][2] and the widely used [limma package][3] for differential expression analysis are also places to look. [1]: https://www.biostars.org/p/92637/#134774 [2]: https://bioconductor.org [3]: https://bioconductor.org/pac ...
written 20 days ago by Ahill1.4k
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Comment: C: Interpretation of linear modelling quality test
... Agree with Kevin's suggestion - curious, re (1) are the before-voom values log2FC from SILAC, TMT intensities, Maxquant LFQs, or MS/MS counts? For something that's a linear-count scale, like MS/MS counts I'd be tempted to log2 transform and look at the residuals after that, just for comparison. In ...
written 21 days ago by Ahill1.4k
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Comment: C: What is the best way to costract a Crispr library
... You might need to provide more details about your experimental goal and methods to get useful feedback on the question. Are you doing a screen to identify modulators of RNA Pol II activity (like a dropout screen), or looking to specifically disrupt function of genes related to RNA Pol II? For the ...
written 27 days ago by Ahill1.4k
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Answer: A: Plotting genes in terms of fold change in different grouping
... Well, one way using traditional R graphics here: # Underscores added to posted space-delimited variable names and values par(mfrow=c(1,2)) stripchart(Fold_Change ~ TRG, data=top, method="jitter", vertical=TRUE, jitter=0.05, col=c(1,2), ylab="log2FC", xlab="Prognosis", pc ...
written 5 weeks ago by Ahill1.4k
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Answer: A: ConsensusClusterPlus for small sample
... You can use consensus clustering on 19 samples - there is no intrinsic minimum sample size required. Typically, for this and other clustering methods the results will be very dependent on how you select informative genes - see the ConsensusClusterPlus manual for [one gene selection approach][1] of ...
written 6 weeks ago by Ahill1.4k
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Answer: A: How to conclude in a significant decrease of coverage depth
... Comparing read depths across individuals might be affected by inter-sample differences in sequencing quality/yield. Tools for identifying structural variations like deletions from read depth are available - take a look at the list of software in Table 1 in [this paper][1] or [this paper][2]. Perha ...
written 6 weeks ago by Ahill1.4k

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