User: rbronste

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rbronste50
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Posts by rbronste

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Comment: C: GRanges object from gene list
... That would we good for refSeq for sure, how would you approach it if just using official gene symbols, such as those in DESeq2 results()? ...
written 3 days ago by rbronste50
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GRanges object from gene list
... Wondering about the most straightforward way to take a list of genes and create a GRanges object, so basically pull the intervals for lets say a list of 500 RefSeq genes? Thanks! ...
genomeintervals genomicranges deseq2 granges bed written 3 days ago by rbronste50
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Comment: C: DESeq2 results export padj sorted
... Thanks for the help! ...
written 4 days ago by rbronste50
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Comment: C: DESeq2 results export padj sorted
... I am a fairly novice user however if you look above at the initial example I did in fact first subset and then sort. Thanks. ...
written 4 days ago by rbronste50
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Comment: C: DESeq2 results export padj sorted
... Well basically in the end I want a BED file of the top 1000 ranges padj<.1, in this list there are many thousands however I just want to export the top thousand by padj. ...
written 4 days ago by rbronste50
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Comment: C: DESeq2 results export padj sorted
... Yes they are GRanges so not sure why its not ordering them properly.  ...
written 4 days ago by rbronste50
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Comment: C: DESeq2 results export padj sorted
... Thanks for the suggestion! While I do get the bed file I am after, it seems to be sorted by chromosome as it only gives me chr1 ranges and not other. Not sure why since I am doing the following: bn_group_male_padj.1_sorted = bn_group_male_padj.1[order(bn_group_male_padj.1$padj<.1), ] export.b ...
written 4 days ago by rbronste50
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DESeq2 results export padj sorted
... When I do the following for some reason the output only includes ranges from a single chromosome or several, while if I look at the padj sorted GRanges in R it includes many chromosomes at the top of the padj list. Is there something I am doing wrong in the sorting and exporting of results? Thanks. ...
deseq deseq2 differential binding analysis written 4 days ago by rbronste50 • updated 4 days ago by Michael Love15k
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Comment: C: Matrix not full rank - DESeq2
... So you're saying the batch information is inherently included in the design anyway right? Thats what I thought.  ...
written 4 days ago by rbronste50
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Comment: C: Matrix not full rank - DESeq2
... In addition this should be insightful: > colData sampleName sex treatment batch 1 MMV1 male vehicle 1 2 MMV2 male vehicle 2 3 MMV3 male vehicle 3 4 FMV1 female vehicle 1 5 FMV2 female vehicle 2 6 FMV3 female v ...
written 4 days ago by rbronste50

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