User: Ahill

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Ahill1.8k
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Posts by Ahill

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Answer: A: Problem with merge data while trying to convert gene names
... Your merged data frame `resdata` has zero rows because `theBM` has zero rows. Your retrieval from Biomart failed to return any rows. I would focus on understanding why your ensembl query `getBM(...)` is failing. If your query had returned rows that matched any of the genes in `resdata$genes`, you ...
written 16 days ago by Ahill1.8k
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Answer: A: At which point should I do a log2 transformation of my iTRAQ LCMS data?
... You should take the first approach: log2 transform the ratios, calculate the mean, then subtract ratios. Reasons to prefer that approach are: - log-ratios in data like iTRAQ should be more normally distributed than the raw-data, and so you can comfortably take a simple arithmetic mean of the log- ...
written 8 weeks ago by Ahill1.8k
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Comment: C: Feature selected-genes vs. differentially expressed genes
... You are certainly right - the GLM approach in DeSeq2 is not a F-test, which would make assumptions of equal variance, etc. that are not made in DESeq2. Assuming you submitted all observed transcripts to the random forest classifier, and not only DESeq2-DE genes, it would be interesting to look at t ...
written 4 months ago by Ahill1.8k
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Comment: C: Feature selected-genes vs. differentially expressed genes
... Yes, to understand differences you would want to compare the differential expression method you've used against the F-test and Gini index methods used by your feature selection, in the context of your experimental design. If this is a one-factor design, for example, and you used ANOVA to select di ...
written 4 months ago by Ahill1.8k
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Comment: C: Multifactor design with Genotype: Is it possible to group all?
... Mods can comment best, but at minimum you can add a direct link to the cross-post here (and vice versa) so that folks know it's in both fora. Like on this post here: https://www.biostars.org/p/322451/#373863. ...
written 6 months ago by Ahill1.8k
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Comment: C: In R scripts of GEO2R which line is responsible for background correction and re
... It would not be safe to say that background correction and duplicate substitution have been done. That would be determined by the original authors who submitted the data to GEO. GEO does not require specific data processing methods as a practice. For many common expression platforms background su ...
written 6 months ago by Ahill1.8k
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Comment: C: Question about comparing expression in different data
... What is the goal of your PCA analysis? Can you describe the organisms and the datasets? If gene X was only expressed in 1 of the 4 organisms, and was therefore an important differentiator among your organisms, is that difference something that you want to account for in your PCA analysis, or not? ...
written 6 months ago by Ahill1.8k
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Answer: C: In R scripts of GEO2R which line is responsible for background correction and re
... From a quick look at the script and at the GEO record for GSE116959, I'd say there are no lines in this code that do either replacement of replicated probes or background correction. The source GEO data appears to be log2-scale quantile-normalized codelink array intensities, so in your script I exp ...
written 6 months ago by Ahill1.8k
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Answer: A: Salmon auxiliary output
... See the Salmon docs: [here][1]. These are gzipped, but in a binary format which the docs describe. Based on a quick look at the descriptions, it appears you could get the contents of these files by reading the uncompressed contents and decoding them using binary constructs available in many script ...
written 6 months ago by Ahill1.8k
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Answer: A: Help with converting gene symbols to gene IDs
... mapIds manual indicates it allows submission of multiple keys, as opposed to one-by-one, and using a different test case that is on hand here, that appears to be much faster: require(AnnotationDbi) require(hgu95av2.db) keys <- head(keys(hgu95av2.db, 'ENTREZID'), 100) # sapply - ...
written 6 months ago by Ahill1.8k

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