User: Ahill

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Ahill980
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Posts by Ahill

<prev • 93 results • page 1 of 10 • next >
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Comment: C: Tools for capturing metadata about experiments and samples
... Very true - unfortunately the definition of a 'good' LIMS seems to depend on who you ask. We get user feedback that LIMS workflows for entering metadata are heavyweight and hard to use. As a result, complete/accurate metadata doesn't get entered. Combination of human and technical factors. A LIMS ...
written 1 day ago by Ahill980
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Tools for capturing metadata about experiments and samples
... Capturing complete and accurate descriptions of experiments and samples is needed for successful bioinformatics analysis, and to enable secondary re-use of experimental data. Experimentalists are busy, and it's not always easy to capture full, correct and consistent metadata annotations for all sam ...
metadata written 1 day ago by Ahill980
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Comment: C: Treatments which upregulate more genes than they downregulate?
... Curious, how are you planning to measure the significant, global, increases in transcription? If using methods like RNA-Seq or arrays, standard ways of normalizing that data make an assumption that overall average gene expression levels remain constant, so may not be able to reliably quantify globa ...
written 1 day ago by Ahill980
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Comment: C: Pairwise comparisons in Differential Expression
... OK, in that case the model (~subject + condition) will fit a two factor model for each gene. Interpretation would depend on if your condition column is technical factor you are looking to normalize away, or if it is a biological factor of interest that you are trying to quantify. What is your main ...
written 2 days ago by Ahill980
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Comment: C: Pairwise comparisons in Differential Expression
... Your metadata does not look like a multi-factor design. It looks like an experiment with a single factor (Day) with two levels (Day 0 and Day 3). Does "Rep" stand for replicate, or is it a designation of paired samples between the days? The model you mention (~ subject + condition) would I believ ...
written 2 days ago by Ahill980
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Answer: A: Geometric Mean of Two Genes in Expression Matrix
... It's not unreasonable to use a geometric mean in the way you describe, and it's certainly been used like this in gene expression analysis. But things to keep in mind. Geometric mean is probably appropriate if your input expression values are on linear scale (not log). The geometric mean is equiva ...
written 3 days ago by Ahill980
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... You could get the probe sequences from the available Affymetrix annotation files, and then paste the sequences into a BLAT tool like the one at UCSC [here][1] to find where the probes map to the latest genome build. [1]: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start ...
written 3 days ago by Ahill980
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Comment: C: Gene level from transcript level expression estimate.
... I'd think the answer is no, depending on how 'gene level estimate' defined. Since transcripts associated with a gene can share exons, I'd think summing counts including overlapping transcripts from the same gene would lead to multiple counting. Or did you mean summing reads over all exons associat ...
written 17 days ago by Ahill980
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Answer: A: KNN and nearest centroid
... No. K-nearest neighbor is a supervised approach where each example to be classified is put into a class by looking at the classes of the K nearest training examples and assigning the example to the majority class. When you say nearest centroids I believe you are referring to methods like K-means o ...
written 5 weeks ago by Ahill980
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Answer: A: Indentical proteins but different Blast results
... BLAST is a *local* alignment method - it can and will give multiple alignments between a single query and target pair, depending on how run. From quick look - I'd guess those are two different sub-sequences of your query (SCO2792) aligning to different sub-sequences of the target (SCO0697), with hi ...
written 8 weeks ago by Ahill980

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