User: aln

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aln290
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Posts by aln

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
... Here is also important message from sctransform adaptation in [Seurat tutorial][1]: > In the standard Seurat workflow we focus on 10 PCs for this dataset, > though we highlight that the results are similar with higher settings > for this parameter. Interestingtly, we’ve found that when usi ...
written 12 months ago by aln290
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Comment: C: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
... So, even if it is computationally feasible it is still good to do PCA, because it suppresses noise? ...
written 12 months ago by aln290
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Comment: C: Non sc-RNA-Seq and Cell Type
... Are you trying to do bulk RNA-seq data deconvolution? If yes, then you need smth like this - [https://github.com/xuranw/MuSiC][1]. Depending on your answer I might suggest few more, but I'm not sure if you just want to check what is the most similar cell type to the particular RNA-seq sample or if y ...
written 12 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290
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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 15 months ago by aln290

Latest awards to aln

Popular Question 11 months ago, created a question with more than 1,000 views. For Identification of APAs (alternative polyadenylation) from standard RNA-seq
Student 16 months ago, asked a question with at least 3 up-votes. For How to answer if the biological process is up or down-regulated?
Supporter 17 months ago, voted at least 25 times.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Mapping Affymetrix IDs to GeneSymbols; Why so many NAs?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Mapping Affymetrix IDs to GeneSymbols; Why so many NAs?
Teacher 3.5 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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