User: Ahill

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Ahill1.8k
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Posts by Ahill

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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 16 days 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 18 days 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 19 days 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 19 days 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 5 weeks 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 5 weeks ago by Ahill1.8k
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Comment: C: MSF Data Analysis
... If you were able to load the MSF file into PD (your screenshot) what other fields not in the screenshot are missing that you need? Are you not able to export or view the complete list of detected proteins from the PD session that's shown in your screenshot? Interested to see what responses the com ...
written 6 weeks ago by Ahill1.8k
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Answer: A: Interpretting a p-value from a fisher exact test?
... Assuming single-tailed test, under the null hypothesis that there is no enrichment of diabetes genes among your DE genes, the probability of a 2x2 table as extreme as yours is high (0.83). This indicates no strong evidence of an association between a gene being DE in your experiment and also being ...
written 6 weeks ago by Ahill1.8k
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Comment: C: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI
... On Windows, presuming the .dmp files are a delimited text format, you can view using the [more][1] command and the corresponding equivalent to 'grep' to search for text in the file is [findstr][2]. Those tools will not require you to load the full files into memory. They won't help you directly wi ...
written 6 weeks ago by Ahill1.8k
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Comment: C: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI
... Google 'gi_taxid_nucl.dmp.gz' yields a 2013 article https://www.polarmicrobes.org/some-things-should-be-easy/ which suggests sqlite or grep. Are you trying to view this file on Windows? Is your primary interest just to see the contents, or to build a database from it and/or link it to other data t ...
written 6 weeks ago by Ahill1.8k

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