User: Taylor, Katie

gravatar for Taylor, Katie
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New User
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Last seen:
9 years, 1 month ago
Joined:
9 years, 2 months ago
Email:
k***@leicester.ac.uk

Posts by Taylor, Katie

<prev • 9 results • page 1 of 1 • next >
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question about limma
... Hi, I just have a quick question. I have been using limma to create toptables looking at differences betwen 6 groups. When I look at the results of the toptables I assumed that positive logFC meant that the gene was upregulated and if negative then it was down regulated. Is this correct? The reason ...
limma written 9.1 years ago by Taylor, Katie90 • updated 9.1 years ago by michael watson IAH-C3.4k
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help with lumi and limma
... Hello, I hope that someone can help me. I have done an experiment using Illumina DASL WG array. I have 48 samples split into 6 groups. I have normalised them all together using lumi; vst followed by quantile normalisation. I have then gone on to use limma to get the topTables for each of the compar ...
limma written 9.1 years ago by Taylor, Katie90 • updated 9.1 years ago by James W. MacDonald50k
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annotating lumi
... Hi, I am trying to annotate my illumina microarray using the following script that I found online. However, I am having some difficulties with it as it is not writing out the annotation data with the normalised data. Also, using this script means that I don't know how to load in the sample file inf ...
microarray annotation normalization probe annotate lumi written 9.2 years ago by Taylor, Katie90 • updated 9.2 years ago by ywchen@jimmy.harvard.edu80
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help with lumi
... Hi, I have just tried to load illumina microarray data into lumi and I added loadAnnotaion=TRUE. However, when I output the data to an .txt document, only the nuIDs are there and the annotation has gone. Does anyone know what i've done wrong? Also, I have 24 samples, with 6 groups. How do I perfor ...
microarray annotation normalization probe lumi written 9.2 years ago by Taylor, Katie90 • updated 9.2 years ago by Pan Du1.2k
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help with multtest and annaffy
... Hi, I have followed the annaffy vignette online and successfully created the HTML documents for annotating the aafExpr dataset. When I try to do the same with my data (GDS2609) which I downloaded from GEO I can only get so far and then R becomes unresponsive and is forced to close. I have copied th ...
annaffy written 9.2 years ago by Taylor, Katie90 • updated 9.2 years ago by James W. MacDonald50k
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Answer: A: help with annaffy package
... Hello, I hope this email finds you well. I am trying to annotate annaffy data and i'm running into some problems. One problem that I faced last week was fixed with your help and I am hoping that you will know what to do with my current problem. I have copied the R output below with the waring messa ...
written 9.2 years ago by Taylor, Katie90
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help with illumina microarray (DASL)
... Hello, I hope that you can help me. I am looking for a way to make a hyperlink table/html document which contains the annotation and data of my illumina microarray. Does anyone know if this can be done? I have found functions where I can look up a range or individual set of genes but I need the who ...
microarray annotation annaffy lumi written 9.2 years ago by Taylor, Katie90 • updated 9.2 years ago by Pan Du1.2k
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help with annaffy package
... Dear Sir/madam, I hope that this email finds you well. I am trying to annotate affymetrix data that I downloaded from GEO. I used the following script which I obtained from the annaffy package vignette but it doesn't work. I have copied the script and R responses below. I would really appreciate yo ...
go annaffy written 9.2 years ago by Taylor, Katie90
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annotation of affymetrix microarray data
... Dear Sir/Madam, I hope that this email finds you well. I am currently undertaking a PhD and I have performed some arrays on the illumina platforms. I have also downloaded some affymetrix data from GEO (GDS2609) which I have successfully analysed in bioconductor. I am new to bioconductor however and ...
annotate annaffy written 9.2 years ago by Taylor, Katie90 • updated 9.2 years ago by Sean Davis21k

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