User: shania90.lk

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shania90.lk10
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Posts by shania90.lk

<prev • 9 results • page 1 of 1 • next >
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Comment: C: VennDiagram from two TestResults matrices
... Thank you for the prompt reply Gordon. I have to find an alternative way then. Maybe create the DGEList for the whole set of samples and apply Voom for separate experimental groups (e.g. subset of root results from the DGEList object and subset of shoot results from the DGEList object, etc.). ...
written 18 months ago by shania90.lk10
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VennDiagram from two TestResults matrices
... Hi all, I would kindly like to know whether it is possible to use two different testResults matrices from the same experiment (e.g. decideTests object from root and shoot) to create a venn diagram using limma vennDiagram() function? I know you might ask why? Because I can easily add the two tissues ...
limma venn diagram written 18 months ago by shania90.lk10 • updated 18 months ago by Gordon Smyth32k
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Comment: C: Enquiry about the summarizeOverlaps() function
... Yes Valerie, you are right. The values correspond with the results from the two runs as well. colSums(assay(ine_counts_2["AT2G25090", "B32_GTTTCG_L001_Aligned"])) B32_GTTTCG_L001_Aligned 11 colSums(assay(ine_counts_1["AT2G25090", "B32_GTTTCG_L001_Aligned"])) B32_GTTTCG_L001_ ...
written 21 months ago by shania90.lk10
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Comment: C: Enquiry about the summarizeOverlaps() function
... Thanks a lot for this Valerie. The gene over-expressed would be AT2G25090. I checked the same with my data for the two runs of summerizeOverlaps(). ..._1 stands for the first run and ..._2 is the second run. > dim(ine_counts_1) [1] 27416 62 > dim(ine_counts_2) [1] 27416 62 > col ...
written 21 months ago by shania90.lk10
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Comment: C: Enquiry about the summarizeOverlaps() function
... Thanks Valerie. No issue with the name. It is not quite a familiar name anyways... Looking forward to your update on the data. Thanks, Shani ...
written 21 months ago by shania90.lk10
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Comment: C: Enquiry about the summarizeOverlaps() function
... Hi Valerie, Thanks for your reply. . The versions I used for first run was GenomicAlignments 1.4.2 but for the second run 1.6.3. For GenomicFeatures first run was in 1.20.6 and for the next 1.22.12. New versions were used for countOverlaps() as well. I saved the TxDb from the first run and loaded ...
written 21 months ago by shania90.lk10
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Comment: C: Enquiry about the summarizeOverlaps() function
... Hi Valerie, Thank you for your response. However, maybe I wasn't clear. I have no issue in getting different results for countOverlaps() and summarizeOverlaps() functions. You are correct on the fact that I wasn't using the same criteria for both. Even if I did, I believe they should not give the s ...
written 21 months ago by shania90.lk10
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Enquiry about the summarizeOverlaps() function
... Hi to the experts, First of all, I would like to thank you for the efforts you put in to the Bioconductor team. Those efforts make the lives of struggling bioinformatics students like me much easy. This is a very naive inquiry about an issue I face with counting features using summarizeOverlaps() ...
summarizeoverlaps rna-seq summarizedexperiment low counts count matrix written 21 months ago by shania90.lk10 • updated 21 months ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: Problem running summarizeOverlaps()
... Hi all, I know this is quite a late reply. But maybe it might help anyone needing help in the future. I realised that the "single.end=TRUE/FALSE" option is now changed to "singleEnd=TRUE/FALSE". The errors I saw in this thread were given to me because of that particular difference. Cheers, Shani. ...
written 21 months ago by shania90.lk10

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