User: songeric1107

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Posts by songeric1107

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Comment: A: DESEQ2 for multi-factor analysis with age(numeric), age and group
... Great, I got it now. One more question, in order to get coefficient for gender and group, I have to convert them to 0,1, instead of F,M, how to interpret the coefficient of gender then? Thank you   ...
written 9 weeks ago by songeric11070
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DESEQ2 for multi-factor analysis with age(numeric), age and group
...   I am trying to use DESEQ2 to estimate the correlation coefficient of gene expression levels with different phenotypes. dds = DESeqDataSetFromMatrix(   countData = round(count),   colData = pheno1,   design = ~ Age+Gender+GROUP)   ddm <- DESeq(dds) my questions is how could I get the coeffi ...
deseq2 written 9 weeks ago by songeric11070
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Answer: A: errors for goseq makeOrgPackageFromNCBI in AnnotationForge
... Could someone tell me how to make database genus = "Mycoplasma", species = "hyorhinis" , which can be used in goseq. thank you       ...
written 2.9 years ago by songeric11070
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Answer: A: errors for goseq makeOrgPackageFromNCBI in AnnotationForge
... Could someone tell me how to make database genus = "Mycoplasma", species = "hyorhinis" , which can be used in goseq. thank you       ...
written 2.9 years ago by songeric11070
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Answer: A: errors for goseq makeOrgPackageFromNCBI in AnnotationForge
... Do you know how to link to David database, they have some similar species there. ...
written 2.9 years ago by songeric11070
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errors for goseq makeOrgPackageFromNCBI in AnnotationForge
... I am trying to make db for Mycoplasma genus = "Mycoplasma", species = "hyorhinis", but I get error, could you please help. makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax_id = "1129369", genus = "Mycoplasma", species = "hyorhinis" ...
go written 3.0 years ago by songeric11070 • updated 2.9 years ago by James W. MacDonald48k
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errors for makeOrgPackageFromNCBI in AnnotationForge
...   I am trying to build the goseq db for Mycoplasma hyorhinis.  Here is what I used: makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir = "."), but I find the e ...
annotationforge written 3.0 years ago by songeric11070 • updated 3.0 years ago by Hervé Pagès ♦♦ 13k
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error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
... I am trying to use the function of fitTimeSeries of metagenomeSeq package.  my dataset are longitudinal dataset of patients. There are multiple data points for each patient   If I use fitTimeSeries to one particular genus, it works. e.g. res = fitTimeSeries(obj=obj,feature="k__Bacteria:p__Firmic ...
microbiome written 4.0 years ago by songeric11070 • updated 4.0 years ago by Joseph Nathaniel Paulson270

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