User: salamandra
salamandra • 330
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Posts by salamandra
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... ah ok, I was doing wrong. thank you! ...
written 7 weeks ago by
salamandra • 330
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... Doing the way you say for 1st example gives only 215 successfully converted ids of a total of 33297 ...
written 7 weeks ago by
salamandra • 330
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... 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
salamandra • 330
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... 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
salamandra • 330
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... 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 ...
written 7 weeks ago by
salamandra • 330
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... 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 ...
written 9 weeks ago by
salamandra • 330
• updated
9 weeks ago by
Kevin Blighe ♦ 66k
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... 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
salamandra • 330
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169
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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 8 months ago by
salamandra • 330
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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 11 months ago by
salamandra • 330
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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 11 months ago by
salamandra • 330
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