User: salamandra

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salamandra330
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Posts by salamandra

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Comment: C: Affymetrix: probeset or transcript cluster?
... ah ok, I was doing wrong. thank you! ...
written 7 weeks ago by salamandra330
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Comment: C: Affymetrix: probeset or transcript cluster?
... Doing the way you say for 1st example gives only 215 successfully converted ids of a total of 33297 ...
written 7 weeks ago by salamandra330
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Comment: C: Affymetrix: probeset or transcript cluster?
... thank you for answering, but meanwhile I tested how many ids were converted successfully in both probeset and transcriptcluster with: sum(!is.na(resultTable$ENSEMBL)) 1st example - GSE75918: *hugene10stprobeset.db*: 327424 ids; *hugene10sttranscriptcluster.db*: 215 ids 2nd example - GSE63296: ...
written 7 weeks ago by salamandra330
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Comment: C: Affymetrix: probeset or transcript cluster?
... I am doing this for studies on GEO, so the array platform varies. Examples: [GSE75918][1] study. the array platform is [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. it works with both transcriptcluster and probeset., but with both there are many NAs. eg of ids: "7 ...
written 7 weeks ago by salamandra330
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Affymetrix: probeset or transcript cluster?
... I used to first normalize Affymetrix microarray data with RMA by 'probeset': oligo::rma(rawData, background=TRUE, normalize=TRUE, target="probeset") and then convert probe ids to gene ids with: select(microarrayPackage, keys = as.character(ids), column = c('PROBEID','ENSEMBL'), keytype='P ...
R oligo microarray affymetrix written 7 weeks ago by salamandra330
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Summarize by gene for agilent microarray data - one color
... I want to normalize agilent data (one color array). Followed limma package user guide, but in the end got some genes repeated for different probes. How can I get data summarized by gene instead of probe? Is it ok, to just average probes of same gene? Code so far: library(limma) library(t ...
R microarray limma written 9 weeks ago by salamandra330 • updated 9 weeks ago by Kevin Blighe66k
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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 5 months ago by salamandra330
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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 8 months ago by salamandra330
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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 11 months ago by salamandra330
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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 11 months ago by salamandra330

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