User: Ahill

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Ahill1.9k
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Posts by Ahill

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Answer: C: negative geo value analysis
... The annotation on this GSM says the reported expression value is: > Normalized signal intensity (Background corrected, log2 transformed, > quantile normalized and base line transformed using the median of all > samples). Since it is a log2-transformed there is nothing intrinsically 'wrong ...
written 10 weeks ago by Ahill1.9k
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Comment: C: getGEO not returning correct sample names
... FWIW it seems this might be an unexpected skip behavior in readr library's [read_tsv][1] for this particular GSE. Which might be worth reporting at the places recommended in the link above. Presuming you have downloaded and unzipped the series matrix file, using the traditional read.delim in place ...
written 11 weeks ago by Ahill1.9k
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Comment: C: getGEO not returning correct sample names
... GEOquery documentation here indicates where to report issues: https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html#reporting-problems-or-bugs ...
written 11 weeks ago by Ahill1.9k
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Answer: A: Code/Tool to locally do sequence alignment
... Yes, you can download, install, and run locally many tools that can match sequences to A. For example, BLAST is available here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download. The best tool to use would depend on your specific requirements. If you want to do pa ...
written 3 months ago by Ahill1.9k
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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 5 months ago by Ahill1.9k
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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 6 months ago by Ahill1.9k
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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 8 months ago by Ahill1.9k
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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 8 months ago by Ahill1.9k
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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 10 months ago by Ahill1.9k
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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 10 months ago by Ahill1.9k

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