User: Amy Mikhail

gravatar for Amy Mikhail
Amy Mikhail460
Reputation:
460
Status:
Trusted
Location:
Last seen:
9 years, 1 month ago
Joined:
12 years, 4 months ago
Email:
a********@abdn.ac.uk

Posts by Amy Mikhail

<prev • 46 results • page 1 of 5 • next >
0
votes
0
answers
415
views
0
answers
how to combine microarray data and phenotype data into a least squares analysis?
... Hi Martin, There are quite a few packages that deal with least squares analysis - also partial least squares. In the latter case there is even one package that is expressly for microarray / gene expression data: the package name is plsgenomics - you can download it from CRAN and it will take your ...
microarray cycle written 9.1 years ago by Amy Mikhail460
0
votes
1
answers
430
views
1
answers
Answer: A: Adding a text label to the classvec colour bar in heatplot
... Hi Kasper, Thanks for the explanation... I looked for Cairo in the capabilities as you suggested, and it says "FALSE". That is with R 2.7.1 on a windows xp operating system - is building with Cairo support something you can choose during the install or does this really only apply if you build R fr ...
written 9.3 years ago by Amy Mikhail460
0
votes
1
answers
443
views
1
answers
Comment: C: Adding a text label to the classvec colour bar in heatplot
... Hi Thomas and Kasper, Many thanks for the tip - I managed to carry out the adjustments I needed in inkscape. I'd still reccomend adding a group label feature to heatplot for general convenience, but modifying in svg format does seem to be a very handy way of finalising things. Forgive my ignoranc ...
written 9.3 years ago by Amy Mikhail460
0
votes
1
answers
443
views
1
answers
Answer: A: Adding a text label to the classvec colour bar in heatplot
... Hi Aedin, What I'd like to do is add group text labels over the colourbar on the top (the rows in my heatplot are genes, the columns are samples). If you look at figures 2 or 3 in the paper below which is co-authored by Robert Gentleman you can see an example of what I mean - the "Relapse" "CCR" l ...
written 9.3 years ago by Amy Mikhail460
0
votes
0
answers
277
views
0
answers
Adding a text label to the classvec colour bar in heatplot
... Dear BioCs, I'm trying to create a heat plot with a matrix containing real time PCR data for just 5 genes. There are 105 samples, belonging to 7 groups (groups are in numerical order). The matrix looks like this (Age is my grouping variable): Gene1 Gene2 Gene3 ...
graph written 9.3 years ago by Amy Mikhail460
0
votes
3
answers
648
views
3
answers
Answer: A: labeling a hclust tree with custom labels
... P.s. - forgot to mention that the below should be done before you create your dist object - then the new sample names will automatically appear in the right place on the hclust dendrogram. Also, appologies - I have always just typed my new sample names but just tried using a vector of names instea ...
written 9.6 years ago by Amy Mikhail460
0
votes
3
answers
648
views
3
answers
Answer: A: labeling a hclust tree with custom labels
... Hi Iain, I'm guessing that the labels currently coming up on hclust are the names of your .cel files? If your expressionset is called my.expressionset, and your desired sample names for images are "Control 1" etc, you could just do: sampleNames(my.expressionset) <- c("Control 1", "Control 2", ...
written 9.6 years ago by Amy Mikhail460
0
votes
4
answers
283
views
4
answers
Answer: A: AveExp" column has dissappeared from limma topTable
... Hi Seth and Gordon, >> Also, what is the difference between an exprSet and an ExpressionSet? >exprSet and ExpressionSet are both classes used to represent microarray data. exprSet is now deprecated in favor of ExpressionSet. >+ seth In a previous post, Gordon has said: "If the first ...
written 10.6 years ago by Amy Mikhail460
0
votes
4
answers
283
views
4
answers
Answer: A: AveExp" column has dissappeared from limma topTable
... Hi Gordon, Thanks for your reply, just tried subsetting without exprs() and it returned a sub-setted exprSet, as you said... So just wondering, when does one actually need to use exprs() and when can I get away without it? Also, what is the difference between an exprSet and an ExpressionSet? Many ...
written 10.6 years ago by Amy Mikhail460
0
votes
2
answers
409
views
2
answers
Answer: A: "AveExp" column has dissappeared from limma topTable
... Hi Marcus, "Mosquito" is a subset of my original exprSet (with some probesets taken out). So it is just a matrix and now that I look, there is no "Amean" element in my fit object. I didn't know that Amean would not be derrived for matrices, thanks for pointing that out. Many thanks, Amy -----Or ...
written 10.6 years ago by Amy Mikhail460

Latest awards to Amy Mikhail

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 115 users visited in the last hour