User: salamandra
salamandra • 280
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Posts by salamandra
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... 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 ...
written 18 days ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... even after translating probe IDs to ensembl/entrez gene ids..thank you ...
written 3 months ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... 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 3 months ago by
salamandra • 280
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... this gets you already normalized data. how do you get raw data from txt file? ...
written 4 months ago by
salamandra • 280
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... I can read bgx, but not the txt file. Do you mean the txt file is not a idat file is that it?
I tried the link you suggested. Specifically tried:
library(GEOquery)
eset = getGEO('GSE26677')[[1]]
but when doing:
exprs(eset)
gets the data already quantile normalized (I know that cause ...
written 4 months ago by
salamandra • 280
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