User: jma1991

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jma199130
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Posts by jma1991

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Comment: C: Improve limma-voom trend fit to noisy data
... +1 for correcting my misconception, thank you. ...
written 9 months ago by jma199130
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Comment: C: Improve limma-voom trend fit to noisy data
... Apologies, I meant X count in *any* N samples, so not filtering based on any group information. That should be independent of the test statistic. You're right about threshold > strategy. I'd like to automate the pre-filtering stage somehow (picking a decent threshold based on the data, HTSFilter ...
written 9 months ago by jma199130
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Comment: C: Improve limma-voom trend fit to noisy data
... Thanks for the reply Aaron, I've just double-checked on some colleagues computers, the second image should definitely have the highlighted areas ( https://ibb.co/eEkGqG ) I guess the discreteness issue could be improved by filtering based on X values being in N number of replicates (rather than av ...
written 9 months ago by jma199130
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Improve limma-voom trend fit to noisy data
... I'm analysing low cell number ChIP-seq data (3 ChIP replicates / 3 Input replicates). The replicates are highly variable due to the low amount of starting material and the number of PCR cycles used for amplification. I am counting reads into windows along the genome and quantile normalising the coun ...
limma voom written 9 months ago by jma199130 • updated 9 months ago by Aaron Lun21k
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Sorry, so are you saying OCT4/POU5F1 has transcripts on different chromosomes? ...
written 11 months ago by jma199130
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Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Actually I'm a bit confused now.. Neither the gene symbol or alias returns the canonical OCT4/POU5F1 gene: library("org.Hs.eg.db") library("TxDb.Hsapiens.UCSC.hg19.knownGene") genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) symbols <- mapIds(org.Hs.eg.db, keys = genes$gene_id, "SYMBOL", k ...
written 11 months ago by jma199130
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Answer: A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... It's called POU5F1B instead of POU5F1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes <- genes(txdb) library("AnnotationDbi") library("org.Hs.eg.db") gene_symbol <- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, columns=" ...
written 11 months ago by jma199130
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Comment: C: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
... Ah that makes sense, thank you for replying ...
written 16 months ago by jma199130
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Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
... :: I originally posted my question on Biostars, but according to the featureCounts website, I should post on this forum for help :: I am using featureCounts (version 1.5.2) to count the number of reads within bins along the genome: featureCounts -R -F SAF --fracOverlap 1 -Q 1 --primary -T 20 ...
featurecounts subread written 16 months ago by jma199130 • updated 16 months ago by Wei Shi2.9k
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Comment: C: strsplit method for DNAStringSet objects
... That's fantastic, thank you very much. I'll test when it becomes available. ...
written 17 months ago by jma199130

Latest awards to jma1991

Scholar 16 months ago, created an answer that has been accepted. For A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene

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