User: saadmurtazakhan

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Posts by saadmurtazakhan

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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... So whats explains the reason for so many gene pairs having value 1? ...
written 11 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... Some of the genes where number of GO terms are not equal always return 1. Is that an accurate value for functional similarity to use? what can be possible turnaround for the same other than not considering those genes altogether? ...
written 11 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... Thanks that helps. ...
written 11 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... But in this example you still have to give semData as an argument. Should I give hsGO or mmGO as semData or would both yeild similar results? ...
written 11 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... I meant what should I specify as semData. In the vignette it uses hsGO as semdata. Since here the data is from two different species what should be semData here. ...
written 11 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... But mgoSim also takes semData as input. How do I bypass that? ...
written 11 months ago by saadmurtazakhan10
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Using GOsemsim to calculate semantic similarity between orthologus genes of two species
... Hi, I know this question has been asked before a long time ago and I don't see an answer of that question in the mailing list or in the vignette of GOsemsim package. So I was wondering what is the easiest possible way of calculating GO semantic similarity value for orthologus gene pairs between two ...
gosemsim gene ontology semantic similarity across species written 11 months ago by saadmurtazakhan10 • updated 11 months ago by Guangchuang Yu800
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Comment: C: Using mgeneSim with Ensembl ids
... What should I change below to make bitr work. bitr(mytestgenes, fromType="ENSEMBLID", toType="ENTREZID", OrgDb="org.Hs.eg.db") Error in bitr(mytestgenes, fromType = "ENSEMBLID", toType = "ENTREZID", : unused argument (OrgDb = "org.Hs.eg.db") ...
written 15 months ago by saadmurtazakhan10
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Comment: C: Using mgeneSim with Ensembl ids
... This is my session info. R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.7 (Final) locale: [1] C attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base      other attached packages: [1] GOSemSim_1.30.3     ...
written 15 months ago by saadmurtazakhan10
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Using mgeneSim with Ensembl ids
... Hi, I have a list of Ensembl ids that I am trying to use with mgeneSim function. Everytime I run it it returns a 0X0 matrix with the following warning message :-  1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL' Here is the code that I use :- mytestgenes <- c("ENSG000 ...
gosemsim ensembl go semantic similarity written 15 months ago by saadmurtazakhan10 • updated 15 months ago by Guangchuang Yu800

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