User: lindfors.erno

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Germany
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3 years, 5 months ago
Joined:
4 years, 7 months ago
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Posts by lindfors.erno

<prev • 8 results • page 1 of 1 • next >
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Comment: C: GEO - Cannot find processed gene expression data ?
... Thanks Gian for your response. My next question is where I can find the column headers for the files that are in the GSE56227_RAW.tar package? To me it looks these files contain ten columns but at least I cannot find any obvious explanation for their content. I think most relevantly I would need ...
written 3.5 years ago by lindfors.erno20
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GEO - Cannot find processed gene expression data ?
... Hi all, I would like to download the processed gene expression data published in the below mentioned publication. Brady RA, Bruno VM, Burns DL. RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model. Subbian S, ed. PLoS ONE. 2015;10(4):e01248 ...
geo rna-seq written 3.5 years ago by lindfors.erno20 • updated 3.5 years ago by Gian350
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Answer: A: BioMart up-to-date with NCBI ?
... Thanks Joe and Emily both for your comments! I tested the file in Jax web site indeed seems to contain most up-to-date conversions. With best regards, Erno Lindfors ...
written 4.1 years ago by lindfors.erno20
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BioMart up-to-date with NCBI ?
... Hi all, I want to convert mouse (MGI) gene symbols to entrez gene ids by using BioMart's R interface (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html). I every now and then come across a mouse gene symbol for which BioMart does not find an entrez gene id but interestingly I can ...
ncbi biomart gene id conversions written 4.1 years ago by lindfors.erno20
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Comment: C: R - GEOQuery getting abandoned ?
... Thanks, recently managed to get GEOquery working! When sending my original message GEOquery was not installed properly in my computer and I was getting an error message that gave an impression GEOquery is not compatible with the R version I am  using. To get GEOquery installed properly the main tr ...
written 4.3 years ago by lindfors.erno20
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R - GEOQuery getting abandoned ?
... Hi all, I understand from a discussion 3 years back (https://www.biostars.org/p/16308/) R 2.13 (or so) is the latest R version that is compatible with GEOQuery package. Does anybody know if there are plans to update this package to fresher R versions? Or could it be so this package is getting aba ...
R geoquery written 4.3 years ago by lindfors.erno20 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: Bioblend - upload_file does not work from command line ?
... Thanks Istvan, recently posted it on https://biostar.usegalaxy.org/p/9210/. With best regards, Erno Lindfors ...
written 4.6 years ago by lindfors.erno20
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Bioblend - upload_file does not work from command line ?
... Hi all, I have been trying to run Galaxy from command line via BioBlend by following an example given in https://www.biostars.org/p/94305/. I have not managed to upload a file from my local computer. More specifically, I am trying to upload a simple flat file that contains one column of integer ...
software error bioblend galaxy written 4.6 years ago by lindfors.erno20

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