User: John Herbert

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John Herbert90
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9 years, 9 months ago
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j**********@bham.ac.uk

Posts by John Herbert

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Comment: C: BLAST E-value
... Dear Alla, Both Richard and Michael have a similar idea to me but to elaborate on their ideas a little. I am not sure your exact biological question but say, for instance, your species are rat and mouse. 1) download the command line version of NCBI blast and install it http://blast.ncbi.nlm.nih.go ...
written 9.8 years ago by John Herbert90
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Comment: C: BLAST search sequence for species ID from R?
... Dear Jos, Michael. To add to Michael's good advice. Roche 454, as I understand it, generates ~450bp reads, so there should be no problem with the default BLAST word size parameter. Once you downloaded your nucleotide database files and your copy of NCBI blastall program, do something like: format ...
written 10.0 years ago by John Herbert90
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Comment: C: A list, a matrix and impute.knn for making data for SAMR
... Hello Elin. Thanks very much for solving my problem, it helps a lot. I knew it would be simple, just like me :-). Actually, that is very useful advice as I was wondering if it told you somewhere what it returned. I should read more thoroughly before posting, sorry. Kind regards, John. -----Origin ...
written 10.3 years ago by John Herbert90
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A list, a matrix and impute.knn for making data for SAMR
... Dear Bioconductors, Please can you help me with small annoying problem. I want to impute a matrix that has 4 columns of data. Using the impute.knn package returns me a list not a matrix. Using as.matrix to return the data returned from impute.knn does not give me the same matrix structure as ...
microarray impute written 10.3 years ago by John Herbert90 • updated 10.3 years ago by Elin Axelsson60
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Answer: A: Statistics for next-generation sequencing transcriptomics
... Hello Michael. Thanks for giving me the chance, I hope, to say something remotely useful here for onece. Firstly, we have recently developed a likelihood ratio statistics for looking at differential expression between two grops cDNA libraries which are effectively the same as comparing Illumina tran ...
written 10.4 years ago by John Herbert90
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Answer: A: Finding differentially expressed genes using Ebayes
... Hi all. Thanks for all your suggestions and help, Sean, James and Saroj. Before I saw the last two messages, I tried this based on the Limma manual and it seems to agree with Samr now. design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2))); colnames(design) <- c("group1", "group2"); fit <- l ...
written 10.6 years ago by John Herbert90
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Finding differentially expressed genes using Ebayes
... Hello. I have 6 gpr files, 3 from cancer and 3 from normals. I have normalised them with printtiplowess and removed the control spots. My question is about finding differentially expressed genes with Ebayes. I have run the code below and get some strange results that are very different to using Samr ...
cancer written 10.6 years ago by John Herbert90 • updated 10.6 years ago by James W. MacDonald52k
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Concordance correlation coefficient and data manipulation
... Hi All. I want to compare array expression data between arrays and samples of similar test conditions. My data contains NaN and inf values and I want to remove these so they are not included in the tests. How is best to do this? I am a Perl-er and new to R, there does not seem an easy way to do it w ...
written 10.7 years ago by John Herbert90 • updated 10.7 years ago by James W. MacDonald52k

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