User: Alex Gutteridge

gravatar for Alex Gutteridge
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Posts by Alex Gutteridge

<prev • 65 results • page 1 of 7 • next >
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Comment: C: DEXSeq for DE of antisense transcription
... Thanks Wolfgang - that looks like it'll do the trick. ...
written 3.1 years ago by Alex Gutteridge650
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DEXSeq for DE of antisense transcription
... I'm looking at ways to detect differential expression of antisense transcripts from stranded RNASeq data. So my first question is: Are there any Bioc packages designed for this type of analysis? I couldn't find any obvious... Obviously one can just count up antisense reads over gene bodies and perf ...
dexseq antisense written 3.1 years ago by Alex Gutteridge650 • updated 3.1 years ago by Wolfgang Huber13k
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Comment: C: DEXSeq continous variable in model
... Hi Alejandro, Just to confirm that your testing was right. I'm not sure what I did wrong the first time I ran the continuous model, but when I reran it over the weekend it worked much better. Apologies for the erroneous bug report! Nice to see my instinct was right and the continuous model gives mu ...
written 3.4 years ago by Alex Gutteridge650
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DEXSeq continous variable in model
... On 30-07-2014 10:13, Alex Gutteridge wrote: > On 29-07-2014 10:00, Alex Gutteridge wrote: >> Hi, >> >> I have a time course RNASeq experiment and I'd like to detect DEU >> between early and late stages. I am trying to use 'Age' as a >> continuous variable in my desig ...
rnaseq timecourse dexseq deseq2 written 3.4 years ago by Alex Gutteridge650 • updated 3.4 years ago by Alejandro Reyes1.5k
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Answer: A: DEXSeq continous variable in model
... On 29-07-2014 10:00, Alex Gutteridge wrote: > Hi, > > I have a time course RNASeq experiment and I'd like to detect DEU > between early and late stages. I am trying to use 'Age' as a > continuous variable in my design, but I'm getting an error which I > suspect is related to this e ...
written 3.4 years ago by Alex Gutteridge650
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DEXSeq continous variable in model
... Hi, I have a time course RNASeq experiment and I'd like to detect DEU between early and late stages. I am trying to use 'Age' as a continuous variable in my design, but I'm getting an error which I suspect is related to this e.g: > summary(sample.data.ipsc[,1:6]) Sample CellType ...
rnaseq go dexseq deseq2 written 3.4 years ago by Alex Gutteridge650
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Comment: C: RRBS question
... Yes, this is exactly what I found. I ended up tweaking maxGap to 10kbp which seemed to give a reasonable result over most regions. Alex Gutteridge On 22.01.2014 16:29, Kasper Daniel Hansen wrote: > Because RRBS data is non-contiguous, you basically have to use the > 'maxGap' argument to do t ...
written 3.9 years ago by Alex Gutteridge650
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RRBS question
... On 21.01.2014 20:48, Gilgi Friedlander wrote: > Hi Alex, > > Sorry to bother you, but I have a question regarding RRBS analysis. > > I saw your post from last year, and also was wondering if bsmooth can > work well for RRBS data, as going to work on such data. > > I wanted to ...
written 3.9 years ago by Alex Gutteridge650 • updated 3.9 years ago by Tim Triche4.2k
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Answer: A: plot methylation figure for end analysis
... On 12.09.2013 08:25, Gia [guest] wrote: > Hi, > I would like to ask if anyone experienced with creating figures from > BS-Seq methylation data for end analysis of genes (or any genomic > features), like what was presented in the following link: > http://www.nature.com/ng/journal/v39/n ...
written 4.3 years ago by Alex Gutteridge650
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Comment: C: limma: correcting for a correlation between contrasts
... Yes, of course you're right T2-T1 is the simpler (correct) way to express that contrast. Muddled thinking on my part. Your second question gets to the heart of my problem: I know that wherever I set the thresholds for determining DE there will be genes that are DE for T2 - Ctrl, but not for T1 - Ct ...
written 4.4 years ago by Alex Gutteridge650 • updated 3.1 years ago by Gordon Smyth32k

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