User: mac

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mac60
Reputation:
60
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Location:
UK
Last seen:
1 year, 7 months ago
Joined:
3 years, 1 month ago
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p*****************@gmail.com

Posts by mac

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Kallisto pseudobam to IGV
... Thank you, I will try this :) ...
written 22 months ago by mac60
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Comment: C: Kallisto pseudobam to IGV
... Thank you for your reply but my understanding is that the kallisto psedobam (which is actually sam) have coordinates based on the transcriptome used to make the index. How can I convert these to genomic coordinates so I can make an indexed bam to view in IGV? ...
written 22 months ago by mac60
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Kallisto pseudobam to IGV
... Hello, I am analysing some RNA-seq data with kallisto and I have created a series of sam files using `--pseudobam` in kallisto. Is there a way of converting these files in a format that can be easily viewed on IGV? Thank you in advance! :) ...
alignment igv kallisto pseudobam rna-seq written 22 months ago by mac60 • updated 15 months ago by mmfansler300
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Comment: C: ChAMP error in EPIC data import
... Hey Yuan, Thank you very much for updating ChAMP and for trying to deal with this bug. Now, using the method = "ChAMP" as you suggested, I get this error data.dir <- file.path("D:/data/") myLoad <- champ.load(directory = data.dir, arraytype="EPIC", method = "ChAMP") Output [= ...
written 23 months ago by mac60
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Comment: C: ChAMP error in EPIC data import
... Just to let you know that I did this and it actually works. Both ChAMP and wateRmelon got a new update a few days ago but the problem persists. Tweaking the pfilter.R as you suggested solves the problem though. Thank you very much for your awesome solution! :) ...
written 2.0 years ago by mac60
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Comment: C: ChAMP error in EPIC data import
... That's great! Thank you very much for this. I will try it again later but I am sure it will work! :) ...
written 2.0 years ago by mac60
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Answer: A: ChAMP error in EPIC data import
... I emailed the developer who said that it is a known problem with the latest version of minfi conflicting with Biobase and suggested downgrading Biobase (which didn't work). For anyone having the same problem, what solved it was installing R 3.2.2 with Biobase 3.4, minfi 1.20.2 and ChAMP 2.6.4. Not ...
written 2.0 years ago by mac60
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Comment: C: ChAMP error in EPIC data import
... Apologies for not replying earlier but as a new user I am limited in the number of posts I can make. I updated R to version 3.4 patched as I was getting [this error][1] when I tried to downgrade minfi as suggested. I then reinstalled bioconductor and ChAMP. I also tried to install all dependencies ...
written 2.0 years ago by mac60
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Comment: C: ChAMP error in EPIC data import
... Yes, I get the same error on Mac when using the ChAMP test data. I have uploaded the Mac sessioninfo at https://pastebin.com/CnZByXjc ...
written 2.0 years ago by mac60
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Comment: C: ChAMP error in EPIC data import
... Thank you very much for your persistence! :) This is what I get on a Mac which is the same error I get on Windows. All packages (and R itself) are up-to-date: > myload <- champ.load(directory = data.dir, arraytype = "EPIC") [===========================] [<<<< ChAMP.LO ...
written 2.0 years ago by mac60

Latest awards to mac

Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: ChAMP error in EPIC data import
Scholar 2.0 years ago, created an answer that has been accepted. For A: ChAMP error in EPIC data import

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