User: Sindre

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Sindre70
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Posts by Sindre

<prev • 16 results • page 1 of 2 • next >
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Finding specific modules compared to consensus modules; cut-off?
... Please see the attached picture; http://imgur.com/a/Waruw. The two arrows indicate two modules apparent in one data set, but not in the consensus data set. However, I don't know how to judge if this is significant?      ...
wgcna written 2.8 years ago by Sindre70
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Answer: A: Wired modules WGCNA cluster dendrogam
... Thank you! I set the soft-thresholding power to 20: http://imgur.com/a/vxkPd Perhaps I should choose 3 instead: http://imgur.com/a/WRVQx ...
written 2.9 years ago by Sindre70
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Wired modules WGCNA cluster dendrogam
... Please see this picture: http://imgur.com/a/cQW6b Why are all the genes "crunched" up at 0.9-1.0? I see the line down at 0.4, before I removed one duplicated row, it was down at 0. Can it be some more trouble with my probes? ...
wgcna written 2.9 years ago by Sindre70 • updated 2.9 years ago by Peter Langfelder2.2k
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Comment: C: Paired samples, two time points, two groups and adjust for a continuous variable
... Thank you very much! This is indeed what I was looking for.  ...
written 3.6 years ago by Sindre70
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Comment: C: Paired samples, two time points, two groups and adjust for a continuous variable
... Ok, thank you. I want to get the genes correlating with VO2max. Specifically, what change in gene expression correlate with the change in VO2max from time 1 to 2. You are correct about the ID. I will re-read the user Guides once more. Thank you! ...
written 3.6 years ago by Sindre70 • updated 3.6 years ago by Gordon Smyth38k
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Comment: C: Paired samples, two time points, two groups and adjust for a continuous variable
... I included the three factors! ...
written 3.6 years ago by Sindre70
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Comment: C: Paired samples, two time points, two groups and adjust for a continuous variable
... Here is data.frame(Status,Time,ID):   Status Time ID IGT A1 2 IGT A1 4 IGT A1 17 IGT A1 21 IGT A1 53 IGT A1 55 IGT A1 61 IGT A1 62 IGT A1 67 ...
written 3.6 years ago by Sindre70
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Paired samples, two time points, two groups and adjust for a continuous variable in edgeR
... I want to find correlations between change in log2(gene expression) and change in log2(VO2max) from time A1 -> B1, adjusted for group and including the fact that the samples are paired. I get this error:   "Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset,  : ...
limma edger written 3.6 years ago by Sindre70 • updated 3.6 years ago by Gordon Smyth38k
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Non-sense results using a continuous variable as predictor in LIMMA
... I have 41 samples in 3 groups (NGT, IGT and T2D). I want to find genes correlating with VO2max, adjusted for age, sex, BMI and diabetic status. Thus, I have 3 continuous variables and one factor. There are no missing values.         Age <- as.numeric(pData.cohort2$Age)         BMI <- as.numer ...
limma written 3.6 years ago by Sindre70 • updated 3.6 years ago by Aaron Lun25k
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How to calculate "This" and "Others" exons in DEXseq
... Hi!   I try to follow this tutorial:   http://www.bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf   Im struggling with this part:   "Each row of the DEXSeqDataSet contains in each column the count data from a given exon (’this’) as well as the count data from the ...
dexseq written 4.9 years ago by Sindre70 • updated 4.9 years ago by Alejandro Reyes1.7k

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