User: José Luis Lavín

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Posts by José Luis Lavín

<prev • 27 results • page 1 of 3 • next >
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Answer: A: DiffBind error
... @Rory, Thank you very much for your help, it works fine. I think I'll follow your advice about how to present the results to the researcher, it's a wise choice. ;-) El Mie, 30 de Enero de 2013, 16:09, Rory Stark escribi?: > Hi again- > > You need to explicitly retrieve the results of the ...
written 6.6 years ago by José Luis Lavín270
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Answer: A: DiffBind error
... Hello again, Thank you very much to Rory and Gordon for your kind and accurate help. Changing the minMembers parameter everything seemed to work fine and I've been able to perform the next steps of the whole analysis. Now I'm struggling with the retrieval of the analysis data; when I try to write ...
written 6.6 years ago by José Luis Lavín270
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DiffBind error
... Dear list, I made a new samplesheet to use with DiffBind with this format: SampleID Tissue Factor Condition Replicate bamReads bamControl Peaks Contrl1 Neural K9 Resistant 1 Control1.bed Contro_input.bed Control1_peaks.bed Contrl2 Neural K9 ...
alignment diffbind written 6.6 years ago by José Luis Lavín270 • updated 6.6 years ago by Rory Stark2.8k
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Comment: C: BAM files to Genomic Ranges object
... Thank you very much Herv?, Your code really got the job done. And thanks also to Steve for his nice comments and Tim for his kind suggestions. With best wishes JL El Mie, 23 de Enero de 2013, 7:40, Hervé Pagès escribi?: > Hi, > > On 01/22/2013 08:29 AM, Steve Lianoglou wrote: >> ...
written 6.7 years ago by José Luis Lavín270
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Comment: C: BAM files to Genomic Ranges object
... Hello Steve, (1) What is the output of `is(cpdens)` ? If it's not a data.frame, this won't work is(cpdens) [1] "list" "vector" "AssayData" "vectorORfactor" head(cpdens) . . . [99841] 1 3 3 3 4 4 2 2 2 1 0 0 0 0 0 1 1 1 1 1 1 1 0 0 [99865] 2 2 0 0 0 0 ...
written 6.7 years ago by José Luis Lavín270
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Comment: C: BAM files to Genomic Ranges object
... Dear all, I'm afraid I have another question derived from the topic of this post. I've used Repitools to calculate Cpg density from my samples, it worked correctly, but now when I try to write the density calculations to a file, I'm unable... Is it possible to do it? Here's how I tried to do it: ...
written 6.7 years ago by José Luis Lavín270
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Comment: C: BAM files to Genomic Ranges object
... First of all I want to thank Herve and Steve for their attention to my questions this time. @Steve, Thanks for the links to Bioconductor manuals, I'll try to read and understand that info as fast & accurately as I'm capable of, trying not to ask very elementary questions in this list ;) @Her ...
written 6.7 years ago by José Luis Lavín270
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Comment: C: BAM files to Genomic Ranges object
... First of all I want to thank Herve Pages and Martin Morgan for their kind answers. And I want to apologize for this delay answering back, but I was offline for a few days... I used Herve code to read my BAM files into GRanges objects, but I don't seem to be able to use that Granges object into the ...
written 6.7 years ago by José Luis Lavín270
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BAM files to Genomic Ranges object
... Hello everybody, I've been told about a very nice R package called Repitools. It has many interesting features but the use of some of them remains a little unclear to me yet. There are some subjects about this tool I'll have to ask about, in this list, but first of all I need to convert some BAM fi ...
alignment convert repitools written 6.7 years ago by José Luis Lavín270 • updated 6.7 years ago by Dario Strbenac1.5k
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Answer: A: DiffBind error
... Thank you Gordon, it was my mistake, I missunderstood the sample sheet and didn't create mine correctly. I think the packege is very very useful and I can't wait to see it working correctly with my samples ;) Best wishes JL El Jue, 20 de Diciembre de 2012, 12:17, Gordon Brown escribi?: > Hi, ...
written 6.8 years ago by José Luis Lavín270

Latest awards to José Luis Lavín

Popular Question 6.6 years ago, created a question with more than 1,000 views. For DiffBind error
Popular Question 6.6 years ago, created a question with more than 1,000 views. For BAM files to Genomic Ranges object
Popular Question 6.6 years ago, created a question with more than 1,000 views. For BAM files to Genomic Ranges object
Popular Question 6.6 years ago, created a question with more than 1,000 views. For DiffBind error

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