User: Maximilian

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Maximilian10
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Posts by Maximilian

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Alternative packages to limma for analysis of microarray datasets
... Hello James, thank you for your suggestions. I will try them out. ...
written 4 months ago by Maximilian10
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Comment: C: Alternative packages to limma for analysis of microarray datasets
... Hello Efstathios, thank you for your answer. As I said in my answer to Ryan, the results for the DEGs with limma are in accord with the gene expression described in the original publication. However, there were some additional, possibly interesting genes in the results and I wanted to see if these ...
written 4 months ago by Maximilian10
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Comment: C: Alternative packages to limma for analysis of microarray datasets
... Hello Ryan, thank you for your answer. No, I don't have concerns about limma' statistical model for my data, the results for the DEGs with limma are in accord with the gene expression described in the original publication Prediction of antibiotic resistance by gene expression profiles available und ...
written 4 months ago by Maximilian10
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Alternative packages to limma for analysis of microarray datasets
... Hello Bioconductor forum, I used Bioconductor package limma for analysis of differentially expressed genes in this Agilent microarray dataset available under https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+GSE59408. Now my question is: are there any alternative packages to limma for analysis ...
microarray limma deg written 4 months ago by Maximilian10 • updated 4 months ago by Bernd Klaus440
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Comment: C: Question regarding best bioconductor package for RNA-seq
... Thanks to both of you for your help! ...
written 6 months ago by Maximilian10
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Question regarding best bioconductor package for RNA-seq
... Dear bioconductor forum, I have a question: I have to analyse RNA-seq data of different RNA read counts mapped to a human reference genome (already in a matrix) for differentially expressed genes between different samples. I found a paper listing the most recent bioconductor packages for this kind ...
rna-seq packages written 6 months ago by Maximilian10 • updated 6 months ago by b.nota290
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Comment: C: Right use of model.matrix?
... Dear Mr. Smyth, thank you for your answer. I apologize for my unclear question. You are right, with the posted code above I find the differentially expressed genes. However, my goal is to find a present/absent pattern for the genes of the mentioned dataset and then use the COBRA toolbox to create t ...
written 10 months ago by Maximilian10
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Right use of model.matrix?
... Dear bioconductor forum, I am using the Agilent RAW .txt microarray data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+GSE59408. My goal is to determine a presence/absence (on/off) pattern for the respective genes on the microarrays. It would be very kind if someone experienced with lim ...
microarray limma agilent lmfit model.matrix written 10 months ago by Maximilian10 • updated 10 months ago by Gordon Smyth31k
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Comment: C: Question about Agilent microarray data measurement
... Dear Mr. Picollo, thank you very much. You helped me a lot! Kind regards, Max ...
written 10 months ago by Maximilian10
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Comment: C: Question about Agilent microarray data measurement
... Dear Mr. Picollo, thank you for your answer. The histogram for UPC.scores.ave looks like this: https://postimg.org/image/nibp6l5rp/ The histogram for UPC.scores looks like this: https://postimg.org/image/h5wjwr2ph/ Does this help to distinguish some kind of presence/absence pattern for the genes ...
written 10 months ago by Maximilian10

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