User: simonjean434

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simonjean43410
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New User
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Canada
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1 year ago
Joined:
2 years, 7 months ago
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s***********@gmail.com

Posts by simonjean434

<prev • 6 results • page 1 of 1 • next >
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maSigPro: how to extract the genes in the same cluster
... Hello, I finally ran maSigPro and Would like to save final results of DE genes in data.frame format. I also would like to extract the genes that are in the same cluster. how can I do that ? Thanks in advance Simon   ...
rnaseq written 19 months ago by simonjean43410 • updated 9 months ago by manuel.hofer0
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maSigPro edesign and error message
... Hi,   I have 6 RNA-Seq samples in different time points and I would like to find DE genes changes during developmental stages. My samples are: Sample Time Replicate Tissue Sample1 day1 1 Liver ...
masigpro written 20 months ago by simonjean43410
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how to design contrast formula in different developemntal stage
... Hello, I am new at EdgeR. I have 6 RNA-Seq samples in different time points and I would like to find DE genes changes during developmental stages. my samples are  Sample Time Tissue Sample1 T1 Liver Sample2 T1 Liver Sample3 T2 Liver ...
edger written 20 months ago by simonjean43410 • updated 20 months ago by Gordon Smyth32k
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Comment: C: DiffBind Normalization by bFullLibrarySize
... Dear Rory, Thanks for your reply. Regarding bFullLibrarySize=FALSE, I understand that you use Sum of all counts in all peaks in each sample. I wonder how you do the normalization of counts before giving count data to EdgeR?   The reason I am asking is because the DE results (FDR10%) that I get th ...
written 20 months ago by simonjean43410
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DiffBind Normalization by bFullLibrarySize
... Hello, I am trying to understand DiffBind in order to use it for my ATAC-seq data analysis and find differential open chromatin sites. could you please explain for me 1- why min number of raw count is 1 and not 0? 2- Regarding normalization, where bFullLibrarySize=FALSE has been used? Thanks ...
atac-seq written 20 months ago by simonjean43410 • updated 20 months ago by Rory Stark2.1k
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SomaticSignatures : could not find scaSNVRanges
... Hello , I am trying to use  SomaticSignatures. I got this error: > sca_vr = scaSNVRanges() Error: could not find function "scaSNVRanges" I am not sure if I did something wrong or this function is not provided in the package. Could you please help me with this?   Thanks J ...
somaticsignatures written 2.7 years ago by simonjean43410

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