User: aln

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aln260
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Posts by aln

<prev • 35 results • page 1 of 4 • next >
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Comment: C: predicting age and gender by using geneexpression
... I think, no ;-) But in general it worked for me, so in cases when you know your samples (e.g. healthy humans) it works nicely. I will definitely check your [post][1]. . [1]: https://gigabaseorgigabyte.wordpress.com/2018/01/26/identifying-an-individual-with-klinefelter-syndrome-in-transcriptome ...
written 11 days ago by aln260
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Comment: C: predicting age and gender by using geneexpression
... For sex prediction I use [massiR][1] package. I had sex data on each sample, so I tested how it works - for my case it predicted everything correctly. [1]: https://bioconductor.org/packages/release/bioc/html/massiR.html ...
written 11 days ago by aln260
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Comment: C: Collapsing probesets to genes on WGCNA
... Just want to add one more comment. There are many ways how to analyze array, with R packages or web-services that were mentioned in this post already. And each analysis step (probes summarization, normalization, annotation etc) can be also done with different tools. You just need to try few of them ...
written 11 days ago by aln260
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Comment: C: Collapsing probesets to genes on WGCNA
... Affymetrix has different types of arrays, where each array has its own annotation. hgu133plus2.db is an annotation for a particular array, that's why it doesn't work with yours. Your array type is Affymetrix Human Gene 1.0 ST. And judging from your answers you didn't have experience with analyzing a ...
written 12 days ago by aln260
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Comment: C: Collapsing probesets to genes on WGCNA
... My example was for the particular Affymetrix array, your probesets ids do not look like typical affymetrix ids. What array do you use exactly? ...
written 12 days ago by aln260
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Comment: C: Collapsing probesets to genes on WGCNA
... Which operation exactly? If you need to annotate your probesets in order to get list of corresponding genes. You can do it like this: library(hgu133plus2.db) select(hgu133plus2.db, probesetsID, "ENTREZID") It will give you 1 to multiple relations list. Then you just check, which probesets ...
written 12 days ago by aln260
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Answer: C: Gene interaction and network analysis tools
... For the quick analysis I would suggest web services: - http://amp.pharm.mssm.edu/Enrichr/ - https://pathview.uncc.edu/ - https://string-db.org/ There are also corresponding R packages for enrichR and pathview. However, keep in mind that most of the online tools are tuned for human, or ...
written 14 days ago by aln260
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Comment: C: clustering cell population from bulk RNA seq ?
... It also sounds for me as deconvolution problem (btw, thanks for the thread reference, @igor). You can look on this: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix/ http://bioconductor.org/packages/release/bioc/html/CellMapper.html Not all the methods are purely based on mathematics, some uses ...
written 17 days ago by aln260
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Answer: A: Collapsing probesets to genes on WGCNA
... `rowGroup` and `rowID` should be of the same length as the error reports. Namely, for each rowID entry you need to have corresponding group ID, it means that groups can be repeated in rowGroup. For microarrays you have cases when one probeset can be mapped to different genes, and when one gene is de ...
written 18 days ago by aln260
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Comment: C: How to answer if the biological process is up or down-regulated?
... 1. > There is no real interpretation here I like this answer:D > Some people, particularly those not used to thinking in terms of networks, might be tempted to say that if genes are up regulated, then the pathway is up-regulated. That's exactly my point, and another problem here is weak und ...
written 20 days ago by aln260

Latest awards to aln

Student 23 days ago, asked a question with at least 3 up-votes. For How to answer if the biological process is up or down-regulated?
Supporter 10 weeks ago, voted at least 25 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Mapping Affymetrix IDs to GeneSymbols; Why so many NAs?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Mapping Affymetrix IDs to GeneSymbols; Why so many NAs?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Mapping Affymetrix IDs to GeneSymbols; Why so many NAs?

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