User: james perkins

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james perkins300
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Posts by james perkins

<prev • 30 results • page 1 of 3 • next >
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Answer: A: replicating ReadqPCR
... Hi Franklin Thanks for pointing out about the plate ID sample label problem - in fact, that should read "plate" only, not plate ID - I will update the vignette appropriately. A couple of issues with your file: 1 your plate ids are more sample descriptions - it is expected that each plate should h ...
written 6.6 years ago by james perkins300
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Answer: A: HTqPCR Normalization
... Hi Carmen, A few questions to get a better idea of the experiment. Firstly, what do you mean by d norm? delta Cq method? I.e. subtraction of reference genes? How many samples do you have? How many conditions? and how many genes in each samples? You say you have different RNA input in every sampl ...
written 7.2 years ago by james perkins300
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Comment: C: GenomicRanges: nearest() for GRanges not returning overlaps
... Thanks a lot Valerie! So precede with "*" is analogous to nearest? Since the nearest will also be preceding it either + or - direction? Jim On 3 July 2012 21:04, Valerie Obenchain wrote: > Hi James, > > Thanks for the bug report. The nearest,GRanges method is currently not > selectin ...
written 7.3 years ago by james perkins300
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Comment: C: GenomicRanges: nearest() for GRanges not returning overlaps
... Thanks, But it appears in the example (using GenomicRanges_1.8.7), the second range is being excluded? I.e. 3-7 matches 5-6 (and 1-3) and thus is > subject2 <- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), + >> > c(3, 6, 12))) > subject2 <- GRanges(seqnames=rep('c ...
written 7.3 years ago by james perkins300
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GenomicRanges: nearest() for GRanges not returning overlaps
... Hi, I read this: https://mailman.stat.ethz.ch/pipermail/bioconductor/2012- June/046287.html However, after reading it I'm a little confused as to what the default behaviour should be when using nearest with '*', and also how to get back to what I believe was the previous, "IRanges" style behaviour ...
iranges written 7.3 years ago by james perkins300 • updated 7.3 years ago by Michael Lawrence11k
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Using readBAM function in segmentSeq
... Dear Thomas, I want to use the seqmentSeq package to look for intergenic expression (lincRNAs etc.) above background. I have case and control samples, with 3 biological replicates. I have bam files (produced using bowtie and samtools) that read in fine with RSamtools. > xx <- readBamGapped ...
go rsamtools written 7.3 years ago by james perkins300 • updated 7.3 years ago by Thomas J Hardcastle180
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Comment: C: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
... Great, Thanks, I'll look out for it! And thanks a lot Andreas for the suggestion of using ensembl exon ids, that sounds good, thanks for all your help. Cheers! Jim On 27 June 2012 17:44, Benilton Carvalho wrote: > That's correct... the summarisation step does use the MPS... and I'll > add ...
written 7.3 years ago by james perkins300
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Comment: C: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
... Sorry, I meant at the rma(target=) level, not the getNetAffx level, which I *assume* uses the mps files to map between ps and transcripts? Cheers, Jim On 27 June 2012 17:27, Benilton Carvalho wrote: > Hi Jim, > > I'll make sure to add the comprehensive MPS as soon as I get more info &g ...
written 7.3 years ago by james perkins300
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Comment: C: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
... Could you expand on that a little? Do you mean you can change the level of confidence of the ps ids mapping to the ENSEMBL gene using biomart? On 27 June 2012 17:30, Andreas Heider wrote: > Also remember, that this will be influenced by your selection of identifiers > in biomart! > > & ...
written 7.3 years ago by james perkins300
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Comment: C: Analysis and annotation (full) of Affymetrix Mouse Exon 1.0 ST arrays
... Thanks Andreas! That's really useful information, I will have a look. Out of interest, did you look at the distribution of expression levels for the different prob-sets? If you are including all probe-sets, I would guess that if there were a lot of predicted/intronic probe sets that aren't expresse ...
written 7.3 years ago by james perkins300

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Popular Question 6.6 years ago, created a question with more than 1,000 views. For vennDiagram in Limma

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