User: Emmanuel Levy

gravatar for Emmanuel Levy
Emmanuel Levy270
Reputation:
270
Status:
Trusted
Location:
Last seen:
1 year, 8 months ago
Joined:
14 years, 4 months ago
Email:
e************@gmail.com

Posts by Emmanuel Levy

<prev • 27 results • page 1 of 3 • next >
1
vote
1
answer
701
views
1
answers
Answer: A: listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not a
... Running the following command, as suggested in a previous post seems to have fixed those issues: BiocInstaller::biocLite('grimbough/biomaRt')     ...
written 21 months ago by Emmanuel Levy270
3
votes
1
answer
701
views
1
answer
listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not available on biomaRt?
... Hi All,   I have been trying to connect to the scerevisiae dataset using biomart and I cannot. I wonder if it's me or a more general problem.   I also notive a very strange behavior with listDatasets, which returns different output when it's called multiple times.   ensembl=useMart("ensembl") ...
biomart bioconductor written 21 months ago by Emmanuel Levy270
0
votes
1
answer
1.1k
views
1
answers
Comment: C: getSequence from biomaRt changes the order of sequences given as input - is it n
... Dear Steffen, Thank you for your answer, I'll send a suggestion to users at biomart then. In the meantime it's really not a problem indeed, the function "match" enables one to reorder things easily. All the best, Emmanuel On 7 January 2013 21:12, Steffen Durinck wrote: > Hi Emmanuel, > ...
written 6.7 years ago by Emmanuel Levy270
0
votes
1
answer
1.1k
views
1
answer
getSequence from biomaRt changes the order of sequences given as input - is it normal?
... Hello, I started using biomaRt and find it really convenient. One thing I noticed is that the function getSequence reorders the sequences when multiple ids are given as input. I'm not sure if this is normal or if I missed an option? Here is what I do: > ensembl.yeast = useMart(biomart="ensemb ...
yeast biomart written 6.7 years ago by Emmanuel Levy270 • updated 6.7 years ago by Steffen Durinck540
0
votes
0
answers
465
views
0
answers
Is it normal that normalize.loess does not tolerate a single NA value?
... Dear all, I have been using normalize.loess and I get the following error message when my matrix contains NA values: > my.mat = matrix(nrow=100, ncol=4, runif(400) ) > my.mat[1,1]=NA > my.mat.n = normalize.loess(my.mat, verbose=TRUE) Done with 1 vs 2 in iteration 1 Done with 1 vs 3 in ite ...
written 10.5 years ago by Emmanuel Levy270
0
votes
1
answer
686
views
1
answers
Comment: C: Normalizing data (that is not in microarray "format")
... Dear Sean, Thank you for your reply. > Reading the help for normalize.loess, it appears that it takes a > matrix as input. You do not need an affy object. Also, note that a This is actually why I tried to use normalize.loess. Although I get warnings, it does normalize my data. The followi ...
written 10.8 years ago by Emmanuel Levy270
0
votes
1
answer
686
views
1
answer
Normalizing data (that is not in microarray "format")
... Dear All, I am trying to normalize data that looks like absolute mRNA expression values (although it's not). This means that I do not have an affy object. I' tried normalize.loess, which partially worked as it gave me the following warning (when I set missing values to 1 it disappears): 50: In me ...
affy written 10.8 years ago by Emmanuel Levy270 • updated 10.8 years ago by Sean Davis21k
0
votes
0
answers
624
views
0
answers
Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
... Thanks for your quick reply - so my first guess was correct: there is no obvious compatibility between GOstats and biomaRt. I'll use NCBI's data then! Best wishes, Emmanuel 2008/9/19 Robert Gentleman : > Hi, > Best to keep discussions on the list. The answer to that is I don't know > ...
annotation go cancer gostats biomart written 11.0 years ago by Emmanuel Levy270
0
votes
2
answers
747
views
2
answers
Comment: C: Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't
... Dear Robert, >> I agree, yet if you type in google: >> site:www.bioconductor.org gostats org.Hs.eg.db > > Well, I guess my point was that google is not a particularly useful tool > for finding documentation for Bioconductor (or indeed most R) packages. They > have documenta ...
written 11.0 years ago by Emmanuel Levy270
0
votes
2
answers
747
views
2
answers
Comment: C: Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't
... Dear Robert, Thank you for your reply. > That seems like an odd place to look for help on Bioconductor packages > (usually the URL would start a bit more like www.bioconductor.org). I agree, yet if you type in google: site:www.bioconductor.org gostats org.Hs.eg.db It seems that there is n ...
written 11.0 years ago by Emmanuel Levy270

Latest awards to Emmanuel Levy

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 16.09
Traffic: 192 users visited in the last hour