User: Sebastien Gerega

Reputation:
370
Status:
Trusted
Location:
Last seen:
10 years, 3 months ago
Joined:
12 years, 5 months ago
Email:
s**@gerega.net

Posts by Sebastien Gerega

<prev • 37 results • page 1 of 4 • next >
0
votes
1
answer
519
views
1
answer
GOstats error
... Hi, Today I received the following error while using GOstats: > hgOver Gene to GO MF test for over-representation 315 GO MF ids tested (15 have p < 0.01) Selected gene set size: 107 Gene universe size: 7005 Annotation package: lumiHumanAll > summary(hgOver) Error in .checkKeys(v ...
annotation go written 10.3 years ago by Sebastien Gerega370 • updated 10.3 years ago by Al Ivens30
0
votes
1
answer
689
views
1
answers
Comment: C: ANOVA p value calculation
... Hi Marc, thanks for your help. I think my confusion came from the fact that I had already performed non-specific filtering to only include genes with GO annotations. So I assumed that all the genes were being included in the test but I now realise the non-specific filtering only ensures that the gen ...
written 10.7 years ago by Sebastien Gerega370
0
votes
1
answer
689
views
1
answers
Comment: C: ANOVA p value calculation
... Hi Robert, sorry about not having included the sessionInfo(). I have included all the required information this time - my sessionInfo() and links to the input data can be found at the end of the email. Here is the code that I am using: entrezUni = read.table("entrezUni.tsv", sep="\t")[,1] sigEntre ...
written 10.8 years ago by Sebastien Gerega370
0
votes
1
answer
689
views
1
answers
Comment: C: ANOVA p value calculation
... Hi, I would like to get a better understanding of exactly how the calculations in GOstats are performed. Does the package use a standard hypergeometric test? If I have the following values: geneIds = 266 universeGeneIds = 1803 and a particular GO term has: size = 124 count = 55 then the associated ...
written 10.8 years ago by Sebastien Gerega370
0
votes
4
answers
875
views
4
answers
Comment: C: ragene10st
... Thanks to all those that offered advice. I have now managed to create an annotation file for rat gene ST arrays. It can be downloaded from: http://sydneybioinformatics.org/download/ragene10st.db.rar in case anyone else is interested in using it. Sebastien Hooiveld, Guido wrote: > Hi Sebastien, ...
written 10.8 years ago by Sebastien Gerega370
0
votes
4
answers
875
views
4
answers
ragene10st
... Thank you Marc and Manhong for your suggestions. I have attempted both methods and run into some problems. Firstly, I was able to build ragene10st.db using the following code: source("http://bioconductor.org/biocLite.R") biocLite("rat.db0") library(AnnotationDbi) fname = "RaGene-1_0-st-v1.EDITED.t ...
annotation go rattus norvegicus chipname cdf probe affy annotationdbi affycompatible written 10.8 years ago by Sebastien Gerega370 • updated 10.8 years ago by Groot, Philip de630
0
votes
2
answers
659
views
2
answers
Comment: C: Annotation for Medicago array (Affy)
... Hi Marc, I guess the problem lies in the fact that I don't know which Annotation file to use. I can't seem to find any that have the appropriate columns. What files were used to generate mogene10st.db and hugene10st.db ? I can find appropriate annotations for Affy 3' arrays but not for the Gene St o ...
written 10.8 years ago by Sebastien Gerega370
0
votes
2
answers
659
views
2
answers
Comment: C: Annotation for Medicago array (Affy)
... Hi Marc and thanks for your help. I've had a look at the SQLForge vignette and there are still a couple issues that are unclear to me. Firstly, for the Rat Gene ST arrays is it possible to use any of the annotation files from the Affymetrix site as input for makeRATCHIP_DB in AnnotationDbi? If not, ...
written 10.8 years ago by Sebastien Gerega370
0
votes
2
answers
659
views
2
answers
Comment: C: Annotation for Medicago array (Affy)
... Hi, I have been analysing human and mouse gene ST chips using a combination of the Aroma package and the hugene10st.db and mogene10st.db annotation packages. Now I am attempting to perform the same on some rat gene ST chips but have unable to find the corresponding annotations. Why is there no ragen ...
written 10.8 years ago by Sebastien Gerega370
0
votes
2
answers
773
views
2
answers
Comment: C: ensembl biomart
... BioMart seems to be down for me at the moment - can't even access http://www.biomart.org/news.html. So out of curiosity I tried your code but got the following error. > listMarts(host="www.ensembl.org/biomart/martservice") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl 52 2 ...
written 11.0 years ago by Sebastien Gerega370

Latest awards to Sebastien Gerega

Popular Question 10.3 years ago, created a question with more than 1,000 views. For topGO w/custom annotation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour