User: reubenmcgregor88

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Posts by reubenmcgregor88

<prev • 23 results • page 1 of 3 • next >
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Comment: C: How do I assess quality of hierarchical clustering?
... Thank you for the reply, and I will be using R indeed so pvclust seems very useful! So this would tell me how robust the nodes in the dendrogram are? Is there a way of carrying out hierarchical clustering but forcing the "cases" and "controls" into groups? If I have interpreted correctly, in this w ...
written 8 months ago by reubenmcgregor8840
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Comment: C: How do I assess quality of hierarchical clustering?
... Yes all the data is one measure on the same scale. ...
written 8 months ago by reubenmcgregor8840
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How do I assess quality of hierarchical clustering?
... Hi all, Very generic question and perhaps a bit of a strange one. I have some data that includes cases and controls. I have created a heatmap and tried some hierarchical clustering using the morpheus software (https://software.broadinstitute.org/morpheus/). What is clear is that no clustering occ ...
hierarchical clustering written 8 months ago by reubenmcgregor8840 • updated 8 months ago by raunakms1.1k
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Comment: C: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... Thank you Friederike, could you please expand on this. Using your example I would like to select (for instance), row 2 based on a)it has NA in columns b and c, b) it has a non-NA in column a. Using the "subset" above I could specific which rows to pull out based on NA but not which rows to pull o ...
written 8 months ago by reubenmcgregor8840
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Comment: C: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... I understand, I guess this is more of a coding question. I am not sure what is wrong with the data, but it seems to be working fine in this case. This is the only format I can get the data in for the moment. I will look into getting the data further upstream so I can QC it. ...
written 8 months ago by reubenmcgregor8840
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Microarray analysis in R (Limma): how to select genes exclusively expressed in one condition.
... Background: I am mining some data using the Limma package to look at differentially expressed genes. I have imported the expression data such that values of 0 are NA. y <- read_excel("exprs.xlsx", na="0") My phenotypic data looks like this: > pData tissue donor ...
R microarray limma written 9 months ago by reubenmcgregor8840 • updated 8 months ago by h.mon28k
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Comment: C: Array Normalization on focussed array in Limma using R
... Yes happy with Gordons response, I guess would be good for others to see his answer too. ...
written 11 months ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Yes it has, sorry did not realise it was forwned upon I will delete post here as it was answered there ...
written 11 months ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Thanks I will try that, although reading the Vignette this will not solve the problem of few proteins which we have chosen specifically due to their high variance between cases and controls? ...
written 11 months ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Thanks Kevin, point taken, I have updated the post. As many posts on here I have come to the project late and do not have all of the information about what analysis was done etc, and we have asked but they are asking to charge us extra for more "bioinformatics services". As mentioned above I have al ...
written 11 months ago by reubenmcgregor8840

Latest awards to reubenmcgregor88

Popular Question 10 months ago, created a question with more than 1,000 views. For annotatePeaks.pl Homer using "RNA"
Great Question 16 months ago, created a question with more than 5,000 views. For ggplot2, point with border
Popular Question 21 months ago, created a question with more than 1,000 views. For ggplot2, point with border

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