User: martin.weihrauch

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Posts by martin.weihrauch

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Comment: C: Analyse only protein_coding genes
... Thank you Aaron, this worked flawlessly. E: Just in case, how could I exclude specific genes? e.g. all genes in this vector c(ENSMUSG00000064370, ENSMUSG00000064341, ENSMUSG00000064351, ENSMUSG00000064363, ENSMUSG00000064345, ENSMUSG00000064367, ENSMUSG00000064368). ...
written 3 days ago by martin.weihrauch0
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Comment: C: Analyse only protein_coding genes
... Thanks for your reply. I've tried to use biomaRt using the approach you linked before as well. I was able to get annotation of all protein_coding genes with Enembl_gene_ids as well, but I was having trouble because my countmatrix somehow contains ~500 annotations more than what biomaRt returns, so t ...
written 4 days ago by martin.weihrauch0
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Analyse only protein_coding genes
... Hi, I'm using featureCounts() to generate the count matrix of my RNAseq experiment and edgeR to do the DGE analysis. Now, during the filtering step I am removing low-count genes like this: fc <- featureCounts(..) counttable <- fc$counts y <- DGEList(counts=counttable) keep <- rowSu ...
edger bioconductor rna-seq written 4 days ago by martin.weihrauch0
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Comment: C: Help with design matrix dealing with 3 variables (DESeq2)
... Dear Michael, Thanks for your advice. I'll read the vignette more carefully. ...
written 5 months ago by martin.weihrauch0
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Comment: C: Help with design matrix dealing with 3 variables (DESeq2)
... The region is the most important part, as it is laser-capture microdissected muscle tissue.  It would be ideal to be able to compare the two different types of muscle at the region of interest vs. the control region. The genotype would be maybe a little secondary for now, but still I want to see wh ...
written 5 months ago by martin.weihrauch0
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Help with design matrix dealing with 3 variables (DESeq2)
... I have an RNA-Seq dataset with 3 variables and 45 samples: muscle (A or B) genotype (WT or TG) region (1 or 2) So I want to compare e.g. WT/A/1 against WT/A/2, but also all other possible comparisons. So far I've used the following design: dds <- DESeqDataSetFromMatrix(counttable, colData = ...
deseq2 rna-seq written 5 months ago by martin.weihrauch0 • updated 5 months ago by Michael Love15k

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