User: René

gravatar for René
René30
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30
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New User
Location:
Netherlands
Last seen:
1 year, 8 months ago
Joined:
6 years, 10 months ago
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Posts by René

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Normalization / size factors of samples with high expression of few genes (viral
... Hi Michael, thanks for the quick response! I doubt that using the viral RNA for normalization will do any good since we are basically just looking at the other half of the sequencing reads compared to the standard normalization. As mentioned, the absorbance measurements after RNA extraction indicate ...
written 22 months ago by René30
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Normalization / size factors of samples with high expression of few genes (viral infection)
... Dear all, I would like to ask for advice concerning the normalization of an RNA-seq dataset that is characterized by extremely skewed libraries due to a viral infection. Briefly, both human and viral RNAs were quantified, and as can be see in the table below, reads from viral RNA (= 10 genes) make ...
normalization deseq2 sizefactors written 22 months ago by René30 • updated 22 months ago by Michael Love26k
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Comment: C: CRLMM on Illumina Human1Mv1_C chips
... Hi Mike, I do have an .sdf file available, however, I doubt that I can make sense out of the grid size as I am not that experienced with SNP arrays and their characteristics. The only 'useful' information I saw in the file can be found below, if you have any idea which chip type is related to this, ...
written 4.8 years ago by René30
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Comment: C: CRLMM on Illumina Human1Mv1_C chips
... Hi Matt, That is also what I had in mind at first, however, the files I have are indeed pretty old (early 2008) and the sample sheet specifies the platform as human1mv1c. Do you know of any other way to test which chip has been used or other potential causes for this error? Best, ​René ...
written 4.8 years ago by René30
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CRLMM on Illumina Human1Mv1_C chips
... Dear all, I am trying to analyze some Illumina beadarray SNP data (human1mv1c) using crlmm and I keep running into the error shown below.  Since my previous attempts on a second, independent cohort (using the human1mduov3b chip) succeeded, my guess is that the problem resides somewhere in the analy ...
beadarraysnp crlmm illumina written 4.8 years ago by René30 • updated 4.8 years ago by Matthew Ritchie800
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easyRNASeq read counts varying when recounting same sample!
... Dear Nicolas, I noticed that my read counts are varying when I count the exact same sample twice. Specifically, genes that have counted reads in the first run are not represented at all (0 counts) in the second run, while others have exactly the same counts! I attached a shortened list of what my ...
biomart easyrnaseq written 6.8 years ago by René30
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Comment: C: How to pool subgroups for makeContrasts() and subsequent limma analysis?
... Dear James, > Hi Rene, > > On 2/6/2013 11:29 AM, Ren? wrote: >> Dear James, >> >> I performed the pooled analysis as you suggested and compared the >> results to a >> pure B - A comparison (no subgroups specified). Interestingly, both >> analyses >> ...
written 6.9 years ago by René30
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How to pool subgroups for makeContrasts() and subsequent limma analysis?
... Hi James, Thanks a lot for clarifying, now I can continue with my analysis. Best regards, Ren? > Hi Ren?, > > On 1/23/2013 4:14 AM, Ren? wrote: >> Dear all, >> >> My current analysis revolves around various groups and their >> subgroups, which is why I would like ...
written 6.9 years ago by René30

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Popular Question 21 months ago, created a question with more than 1,000 views. For CRLMM on Illumina Human1Mv1_C chips

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