User: john seers IFR

gravatar for john seers IFR
Reputation:
810
Status:
Trusted
Location:
Last seen:
10 years, 3 months ago
Joined:
13 years, 8 months ago
Email:
j*********@bbsrc.ac.uk

Posts by john seers IFR

<prev • 81 results • page 1 of 9 • next >
0
votes
2
answers
773
views
2
answers
Answer: A: Problems with biomaRt
... Hi I had similar problems which I raised in this forum a month or so ago. The solution was, I think, to specify both the "--internet2" and the "http_proxy" options on the command line. It appears that just the one option is not sufficient for bioMart and one of the packages it uses (RCurl?). Th ...
written 10.3 years ago by john seers IFR810
0
votes
1
answer
591
views
1
answers
Answer: A: Help with contrast matrix
... Hi Jenny >3 Does the number of coef correspond to the order of the contrasts listed in the contrast.matrix command? for example, coef=3 >corresponds to the contrast "wt5hr-ste5hr"? That is correct. Which means "wt5hr-wt4hr" is not your first contrast. >Resultfile <- topTable(fit2, ...
written 10.3 years ago by john seers IFR810
0
votes
2
answers
647
views
2
answers
Answer: A: Limma - GenePix
... Hi All Ah!. Perhaps, "the header removed" does not mean removing the header row. Just the n lines of Genepix information? Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Gordon K Smyth Sen ...
written 10.3 years ago by john seers IFR810
0
votes
2
answers
647
views
2
answers
Comment: C: Limma - GenePix
... Hi Gordon I am sure this is going to end up somewhere silly but here goes. :) >To read microarray data in a generic format, you have to tell limma the >column names of the data columns you want it to read. Yes, understood. >This means that you have to check first yourself, eg using Ex ...
written 10.3 years ago by john seers IFR810
0
votes
2
answers
647
views
2
answers
Answer: A: Limma - GenePix
... Hi Just out of curiosity, how does limma know how to match the names? Where do the column names come from? I am missing something here ... Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Go ...
written 10.3 years ago by john seers IFR810
0
votes
1
answer
364
views
1
answers
Answer: A: Retrieve aminoacid sequence starting from protein identifier
... Hi Giulio Have a look at getSEQ and getGI in the annotate package. I think they do what you want. These two lines were lifted out of one of them I think: > accession="P10451" > seq <- readLines(paste("http://www.ncbi.nlm.nih.gov/entrez/batchseq.cgi?", "cmd=&txt=on&save=&cf ...
written 10.3 years ago by john seers IFR810
0
votes
2
answers
683
views
2
answers
Answer: A: Limma - GenePix
... Hi Juana Having read your email more closely perhaps what I sent you is not useful. Unless there is some feature of limma I do not know about I do not think what you are doing can work. I think read.maimages needs the header names at some point, so if you have not got them you will have to suppl ...
written 10.3 years ago by john seers IFR810
0
votes
2
answers
683
views
2
answers
Answer: A: Limma - GenePix
... Hi Juan If you look at the code for read.maimages there appear to be four entries for genepix: genepix = , (Not sure what this does). genepix.mean = list(R = "F635 Mean", G = "F532 Mean", Rb = "B635 Median", Gb = "B532 Median"), genepix.median = list(R = "F635 Median", G = "F532 Median", R ...
written 10.3 years ago by john seers IFR810
0
votes
1
answer
545
views
1
answers
Comment: C: Variance
... Hi David Ah, yes. which.min is better. For instance, type in > myvars[which.min(myvars)] geneA 0.18827 > Regards John -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of David martin Sent: 22 June ...
written 10.3 years ago by john seers IFR810
0
votes
1
answer
545
views
1
answers
Answer: A: Variance
... Hi Something like this? geneA<-c(-6.19, -5.74, -5.82, -5, -5.59) geneB<-c(-6.33, -5.32, -5.6, -4.88, -5.39) geneC<-c(-6.15, -6.07, -5.6, -4.88, -5.9) geneD<-c(-6.57, -6.11, -6.36, -5.36, -5.96) geneD<-c(-6.74, -6.2, -5.49, -5.35, -5.95) geneE<-c ...
written 10.3 years ago by john seers IFR810

Latest awards to john seers IFR

Popular Question 10.3 years ago, created a question with more than 1,000 views. For Protein/peptide mass

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 208 users visited in the last hour