User: c.lieftink@nki.nl

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Posts by c.lieftink@nki.nl

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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi Michael, Thanks a lot! Best regards, Cor ...
written 4.7 years ago by c.lieftink@nki.nl20
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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi Michael, Yesterday I ran an analysis of 15 mutant cell lines against 226 wildtype/unknown cell lines for 1200 hairpins. It took 8 hours on my home computer, but I have the results! :-) Thanks again. Cor   ...
written 4.7 years ago by c.lieftink@nki.nl20
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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi Michael, Thanks again for your quick response! I downloaded the development version, and was now able to process the data also in case of different number of replicates for the two status conditions! Best regards, Cor ...
written 4.7 years ago by c.lieftink@nki.nl20
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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi Michael, It runs fine with 3 replicates in each status condition, however adding a fourth in only the 0 (=wildtype) condition gives the error not full rank. > as.data.frame(colData(dds)) status rep time m0.EFO21.t0 0 1 0 m0.EFO21.t1 0 1 1 m0.JHESOAD1 ...
written 4.7 years ago by c.lieftink@nki.nl20
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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi Michael, Sorry to bother you again. Your solution works fine when I have equal number of mutant and wildtype cells. However if not, I get  again the error "the model matrix is not full rank". Do you know of any alternative design to deal with that as well? Best regards, Cor ...
written 4.7 years ago by c.lieftink@nki.nl20
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Comment: C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hello Michael, Thank you for your quick response! Best regards, Cor ...
written 4.7 years ago by c.lieftink@nki.nl20
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
... Hi all, I would like to use DESeq2 for the analysis of a pooled shRNA screen to identify mutation specific lethals. The design of the experiment is a number of mutant cell lines and a number of wildtype cell lines. For every cell line there is a t0 measurement and t1 measurement. Interesting hairpi ...
deseq deseq2 written 4.7 years ago by c.lieftink@nki.nl20 • updated 4.7 years ago by Michael Love25k
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Definition of the CellHTS2 normalizePlates parameter scale
... Hi Elin, Thank you very much for the quick response and elaborate and clear explanation! Cor -----Original Message----- From: Elin [mailto:elin@ebi.ac.uk] Sent: Wed 9/17/2008 11:08 To: Cor Lieftink Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Definition of the CellHTS2 normalizePlate ...
normalization cellhts2 written 11.1 years ago by c.lieftink@nki.nl20
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Definition of the CellHTS2 normalizePlates parameter scale
... Hello everyone, The cellHTS2 method normalizePlates has a parameter called "scale". The two values are "additive" vs. "multiplicative". Although it seems be some basic statistical knowledge I am not able to find a clear definition of additive versus multiplicative data scale. Can anyone provide me ...
normalization cellhts2 written 11.1 years ago by c.lieftink@nki.nl20 • updated 11.1 years ago by Elin Axelsson60

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Great Question 4.6 years ago, created a question with more than 5,000 views. For With DESeq2 "Not full rank" Error with design ~ line + time + condition
Popular Question 4.6 years ago, created a question with more than 1,000 views. For With DESeq2 "Not full rank" Error with design ~ line + time + condition

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