User: Ahill

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Ahill1.1k
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Posts by Ahill

<prev • 99 results • page 1 of 10 • next >
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Comment: C: meta data analysis for clustering
... What's the readout from the screens - is it multiparametric (high content imaging, RNA-Seq, ...) or single parameter (cell survival, reporter assay?). I'm not clear on what signatures you are looking for by clustering - are these clusters of genes that have common readout patterns across RNAi treat ...
written 2 days ago by Ahill1.1k
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Answer: A: How do I add ">" symbol to FASTA headers?
... sed 's/^\([^acgt]\)/>\1/' > ...
written 11 days ago by Ahill1.1k
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Answer: A: The use of "and" in bioinformatics literature
... The "and" may not guarantee it was normalized first and log2-transformed second... Either approach could have been used, so if the order is important to you I would look more closely at the methods section of the paper for the details of the algorithms used. Example: for Affy oligo arrays, MAS5 m ...
written 29 days ago by Ahill1.1k
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Comment: C: Why do they use ratios for differential expression analysis?
... I'd say commonly accepted expression measurements would be considered ratio scale, not interval scale. Consider RNA-Seq, where the fundamental measurement is a count of sequence reads. This measure has a meaningful zero point, and DE ratios between mapped counts are meaningful (for example, under ...
written 6 weeks ago by Ahill1.1k
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Comment: C: Plotting ROC curve for categorical variables
... In the results you pasted, it looks like you have a single prediction of 7 cases, with overall accuracy = 4/7, if 'Reported' column is the ground truth. This observation would define a single point on a ROC curve. Plotting a ROC curve requires a classifier/predictor that can be parameterized to ad ...
written 6 weeks ago by Ahill1.1k
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Comment: C: Using linear mixed models for genome-wide interaction analyses
... Perhaps [EPACTS][1] / [EMMAX][2] ? EPACTS link provides instructions on file formats needed. [1]: https://genome.sph.umich.edu/wiki/EPACTS [2]: http://genetics.cs.ucla.edu/emmax/index.html ...
written 11 weeks ago by Ahill1.1k
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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 12 weeks ago by Ahill1.1k
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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 12 weeks ago by Ahill1.1k • updated 4 weeks ago by Biostar ♦♦ 20
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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 12 weeks ago by Ahill1.1k
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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 12 weeks ago by Ahill1.1k

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