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User: salamandra

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salamandra • 320
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Posts by salamandra

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Comment: C: Does Gene length corrected TMM [GeTMM] violate any assumptions of TMM normalizat
... I understand your point, but why then in the article they use GeTMM for DE as well? See figure 7 [here][1] [1]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2246-7 ...
written 12 weeks ago by salamandra • 320
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Which annotation package to use to mapIds() on HuEx-1_0-st-v2 microarray platform?
... when running: microarrayPackage = 'pd.huex.1.0.st.v2' mapIds(eval(parse(text = microarrayPackage)), keys = ids, column = 'ENSEMBL', keytype='PROBEID') I get the error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mapIds’ for sign ...
R bioconductor microarray written 6 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... From GeneAnnot site we can see that different probe sets that target same gene have variable numbers of same probes. For example for gene MAPK1 there is: [1552264_a_at probe set][1] has probes 1 to 11, while [224621_at probe set][2] has probes 1 to 3 and 8 to 11. For same probe set, different combin ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... If they are different isoforms, doing an average of two might not be appropriate cause one might no be expressed and that brings gene expression down.. ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... I saw in another post that one probe-set targets one exon. So, does it mean that two probe-sets may be targeting two different exons of same gene, and that's why we get even after summarizing a U133 array different probe set ids corresponding to same ensembl gene id? Or is there only one gene per pr ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... even after translating probe IDs to ensembl/entrez gene ids..thank you ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... could you then provide that info please? so in this case, by doing rma() automatically summarizes by transcript instead of gene is that it? ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... I tried both: array is Affymetrix Human Genome U133 Plus 2.0 Array from this study: [GSE28799][1] Code is: library(oligo) library(GEOquery) platform = 'HG-U133_Plus_2' # specific affymetrix microarray platform dataDir <- 'D:/Tania_2/PhD/CSCs/data/' studyId <- 'study10' ...
written 9 months ago by salamandra • 320
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Comment: C: Human Exon array probeset to gene-level expression
... I am trying to summarize on gene level with `target=core`, but get this error: `Error in .local(object, ...) : unused argument (target = "core")`, even when specifying `oligo::rma(` Do you know why is this happens? ...
written 9 months ago by salamandra • 320
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Comment: C: Cannot read Illumina data (.bgx and .txt format) in R for microanalysis
... this gets you already normalized data. how do you get raw data from txt file? ...
written 10 months ago by salamandra • 320

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