User: martin.hoelzer

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20
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New User
Location:
Germany
Last seen:
1 year, 7 months ago
Joined:
2 years, 1 month ago
Email:
m*************@uni-jena.de

Posts by martin.hoelzer

<prev • 11 results • page 1 of 2 • next >
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DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
... Hello,  I already found out how to select specific comparisons from the object resulting from the DESeq() function dds <- DESeq(ddsHTSeq) using the 'contrast' variable in the 'results' function like this: deseq2.res <- results(dds, contrast=c("condition","treated_A","untreated_A")) With ...
deseq2 written 20 months ago by martin.hoelzer20 • updated 9 months ago by ruy204github0
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Comment: C: GOexpress: GO_analyse function throws Error: Space required after the Public Ide
... Hi Kevin,  this solves my issue, thank you very much.  best, Martin ...
written 20 months ago by martin.hoelzer20
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Answer: A: GOexpress: GO_analyse function throws Error: Space required after the Public Ide
... Hi Kevin,  the ensembl webpage is now accessible again via www.ensembl.org, but this was not the problem. The command  ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl") still throws this error. My sessioninfo() tells R version 3.2.2 and biomaRt_2.24.1/GOexpress ...
written 20 months ago by martin.hoelzer20
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Answer: A: GOexpress: GO_analyse function throws Error: Space required after the Public Ide
... Hi Kevin,  thanks for your reply, I just tried several times ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl") but also here I just get: Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ...
written 20 months ago by martin.hoelzer20
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GOexpress: GO_analyse function throws Error: Space required after the Public Identifier
... Hello,  some time ago I used the Go_analyse function of the GOexpress package with Ensembl IDs as input, so the automatic mapping should be no problem. Now I get the following error: > GO_results <- GO_analyse(eSet = minimalSet, f = "Treatment") First feature identifier in dataset: ENSG0000 ...
goexpress written 20 months ago by martin.hoelzer20 • updated 20 months ago by kevin.rue200
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Answer: A: GOexpress: use DESeq2 data object as input
... Hi,  I tested it now and it seems to be working, thanks! So what I did was just the following to create from my DESeqDataSet a simple ExpressionSet, so according to the example table above: Start from: dds <- DESeq(ddsHTSeq) Followed by: exprs <- counts(dds, normalized=T) # get normaliz ...
written 2.1 years ago by martin.hoelzer20
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Answer: A: GOexpress: use DESeq2 data object as input
... Dear Kevin,  thanks for your fast reply and sorry for the maybe confusing description. Lets assume I have the following raw read counts of six mouse RNA-Seq samples in two conditions (lets say 'control' and 'treated', 3 replicates each), so a table like this:   control_rep1 control ...
written 2.1 years ago by martin.hoelzer20
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GOexpress: use DESeq2 data object as input
... Hello,  I am trying to use the GOexpression package described here: http://www.bioconductor.org/packages/release/bioc/vignettes/GOexpress/inst/doc/GOexpress-UsersGuide.pdf I am followed the manual at first and everything works fine with the test data set (microarray data I suggest). Now I wanted ...
deseq2 expressionset goexpress written 2.1 years ago by martin.hoelzer20
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Answer: A: GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same l
... Hi, yep, for me it is also working now again. Thanks for the help and the information.  Cheers, Martin ...
written 2.2 years ago by martin.hoelzer20
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Answer: A: GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same l
... Dear Weijun, thank you for your reply. Now I can settle down a bit, because I was really thinking about what I am doing wrong after several new R installations and different versions testing. :) Hopefully this can be fixed soon. Thanks and kind regards, Martin  ...
written 2.2 years ago by martin.hoelzer20

Latest awards to martin.hoelzer

Scholar 20 months ago, created an answer that has been accepted. For A: GOexpress: use DESeq2 data object as input
Scholar 2.1 years ago, created an answer that has been accepted. For A: GOexpress: use DESeq2 data object as input

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