User: Ahill
Ahill • 1.8k
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Posts by Ahill
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
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... 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
Ahill • 1.8k
2
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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
Ahill • 1.8k
1
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1
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240
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... 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
Ahill • 1.8k
Latest awards to Ahill
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10 weeks ago,
created a post with more than 5 votes.
For A: Why gene expression data should be log2 transformed?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For convert MACH .mlprob to Oxford .gen format
Great Question
21 months ago,
created a question with more than 5,000 views.
For Resources for flow cytometry bioinformatics
Appreciated
22 months ago,
created a post with more than 5 votes.
For A: Why gene expression data should be log2 transformed?
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: Why gene expression data should be log2 transformed?
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Centurion
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