User: Ahill
Ahill • 1.4k
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Posts by Ahill
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
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... 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
Ahill • 1.4k
2
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... 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
Ahill • 1.4k
0
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... 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
Ahill • 1.4k
0
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... 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
Ahill • 1.4k
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