User: Sabet, Julia A

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Posts by Sabet, Julia A

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Comment: C: cummeRbund graphics not working
... Yay thank you so much!! ☺ From: Loyal A. Goff [mailto:lgoff@csail.mit.edu] Sent: Friday, July 25, 2014 3:33 PM To: Sabet, Julia A Cc: bioconductor@r-project.org Subject: Re: [BioC] cummeRbund graphics not working Hi Julia, In your scripts, you appear to be placing the created plot objects into a v ...
written 5.1 years ago by Sabet, Julia A180
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cummeRbund graphics not working
... Hello all, I have been trying to use cummeRbund for a long time but I have not been able to get the graphics (plots) to show up either by "windows()" or by making a pdf file. I am using R on windows. I am pretty new to R so I am not sure if this is a general R issue or some issue specific to this ...
cummerbund written 5.1 years ago by Sabet, Julia A180 • updated 5.1 years ago by Loyal Goff140
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EB Seq conditions
... Hello, I am using EB Seq and I am wondering if there is a way to specify the conditions by referring to a text file that I have read into R which lists all the samples and their conditions. I have done this for other R packages but can't figure out how to do it in this case- I get errors. I figure ...
written 5.2 years ago by Sabet, Julia A180
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Comment: C: no significant differences in gene expression-limma
... Thanks for your help. It just occurred to me- should plotMDS be done on normalized data, raw data, filtered data? All of the above? ...
written 5.5 years ago by Sabet, Julia A180 • updated 4.6 years ago by Gordon Smyth38k
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Comment: C: no significant differences in gene expression-limma
... Thank you for your explanation, Gordon!  I was finally able to figure out how to generate the plot using the following code, with labels corresponding to my 3 different diet groups (the example on the help page definitely helped): >plotMDS(mds, col=c(rep("black",12), rep("red",12), rep("blue", ...
written 5.5 years ago by Sabet, Julia A180 • updated 4.6 years ago by Gordon Smyth38k
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Comment: C: no significant differences in gene expression-limma
... Thank you Gordon.  I looked up the R documentation for plotMDS and did the following code, using my normalized eset, and came up with the following error.  Could you or someone else tell me what I did wrong and if I am missing some code?  I am new to R and had never heard of plotMDS before...I don't ...
written 5.5 years ago by Sabet, Julia A180 • updated 4.6 years ago by Gordon Smyth38k
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no significant differences in gene expression-limma
... Hi all, I have just analyzed some Affymetrix Mouse Gene 2.0 ST arrays using limma and I found no significantly differentially expressed genes (according to adjusted p value being <0.05).  I tried a few different filtering methods, including no filter, and I tried to analyze males and females sepa ...
annotation written 5.5 years ago by Sabet, Julia A180 • updated 4.6 years ago by Gordon Smyth38k
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limma design matrix missing a Date column
... Hello, I am trying to make a design matrix for limma and include date to account for batch effects, but when I construct the matrix, one of the dates is excluded for some reason (1/7/2014). I am interested in comparing the effects of diet within males and females separately. Any ideas why this date ...
limma dss written 5.5 years ago by Sabet, Julia A180 • updated 5.5 years ago by James W. MacDonald50k
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Comment: C: filtering probes in affymetrix data
... Thank you. I couldn't figure out how to filter out controls. What would the code be to filter out both controls and background using kOverA as you suggested? Thanks Julia -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Thursday, February 13, 2014 6:21 PM To: Sab ...
written 5.5 years ago by Sabet, Julia A180
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Comment: C: filtering probes in affymetrix data
... It gives me this: Features Samples 2426 36 -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Thursday, February 13, 2014 5:47 PM To: Sabet, Julia A Cc: bioconductor at r-project.org Subject: Re: [BioC] filtering probes in affymetrix data How many probeset ...
written 5.5 years ago by Sabet, Julia A180

Latest awards to Sabet, Julia A

Popular Question 5.1 years ago, created a question with more than 1,000 views. For cummeRbund graphics not working
Popular Question 5.1 years ago, created a question with more than 1,000 views. For no significant differences in gene expression-limma
Popular Question 5.1 years ago, created a question with more than 1,000 views. For cummeRbund graphics not working

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