User: stinehedensted

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Posts by stinehedensted

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Help to understand my contrast.matrix and to interpret my topTable results
... Thank you for your response!  Actually is have 60 rows in my design matrix, R just prints a truncated version.  > dim(design) [1] 60 31 > dim(Array_benigntissue2[,4:63]) [1] 33297    60 I have tried to look into your suggestion of using a blocking design. I understand from the Limma User ...
written 6 weeks ago by stinehedensted0
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Comment: C: Help to understand my contrast.matrix and to interpret my topTable results
... Thank you for your response!  Actually is have 60 rows in my design matrix, R just prints a truncated version.  > dim(design) [1] 60 31 > dim(Array_benigntissue2[,4:63]) [1] 33297    60 I have tried to look into your suggestion of using a blocking design. I understand from the Limma User ...
written 7 weeks ago by stinehedensted0
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Help to understand my contrast.matrix and to interpret my topTable results
... Hi I am trying to analyse a microarray dataset from GEO.  The data is already normalized and log2 transformed. I have 30 paired patient samples of benign prostate epithelia and stroma tissue. The data is grouped like this:  Patient Treatment 1 B 1 sB 2 ...
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Answer: A: Differential expression of nomalised and log2 transformed data in limma
... Hi Gavin,  Thank you for your reply. You are totally right, I was using the wrong function. I have now turned the dataframe into a numeric matrix. I ordered all the samples in the csv file, so I know fore sure, that the 25 first samples are from cancer, and that the last 25 sampls are from stroma.  ...
written 7 weeks ago by stinehedensted0 • updated 7 weeks ago by Steve Lianoglou12k
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Differential expression of nomalised and log2 transformed data in limma
... Hello   I have normalized and log2 transformed RNA microarray data from GEO, and I want to do differential gene expression analysis with the limma package in R.  My dataset contains 25 samples of cancer og 25 samples of stroma. Each sample have 33297 gene expression values.  I've loaded my data ...

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