User: Jakob Hedegaard

gravatar for Jakob Hedegaard
Reputation:
160
Status:
Trusted
Location:
Last seen:
7 years ago
Joined:
13 years, 5 months ago
Email:
j**************@agrsci.dk

Posts by Jakob Hedegaard

<prev • 15 results • page 1 of 2 • next >
0
votes
0
answers
521
views
0
answers
RNA-Seq - analysis of time series data?
... Hi, I wonder how to analyze a RNA-Seq dataset of a time-series experiment. The dataset origin from a challenge experiment with 4-6 samples per time point (T00,T06,T12,T24 and T48) from two series of challenge (with one of two different serotypes). In total 48 individual samples and two factors, ti ...
genetics edger written 7.1 years ago by Jakob Hedegaard160
0
votes
0
answers
502
views
0
answers
Experimental design for RNA-Seq
... Hi Mick, After quantification of each library using qPCR, we prepared a 20 pM dilution in hyb-buffer. This was followed by pooling of the 12 plex sets producing a 20 pM solution of 12-plex libraries, which according to Illumina should be stable for 2-3 weeks. From this 20 pM stock solution we then ...
sequencing qpcr cancer written 7.5 years ago by Jakob Hedegaard160
0
votes
1
answers
547
views
1
answers
Comment: C: Experimental design for RNA-Seq
... Hi, We have just completed the sequencing of RNA-Seq libraries from a porcine challenge experiment: two treatments (bacteria) and 5 time points after challenge (T0,T6,T12,T24,T48 hours pi) - a total of 48 samples (5-6 samples/treatmentXtime). A single RNA-Seq library has been generated from each sa ...
written 7.5 years ago by Jakob Hedegaard160
2
votes
2
answers
1.1k
views
2
answers
edgeR - technical and biological replication
... Hi, I have a RNA-Seq dataset produced on a Illumina GA and wonder how to account for both technical and biological replication using edgeR. The dataset consist of 48 individual samples (time series with 4-6 biological replica per time point, 9 time points in total) which have been sequenced in three ...
edger written 7.6 years ago by Jakob Hedegaard160 • updated 7.6 years ago by Gordon Smyth32k
0
votes
1
answer
356
views
1
answer
Limma - using both array and spot weights in lmFit
... Hi List I use spot weights (binary) to A) ignore spots "Not found" in GenePix during normalization: RG <- read.maimages(fnames, source="genepix", path=datadir, columns=columns, other.columns=other.columns, wt.fun=wtflags(weight=0,cutoff=0)) MA <- normalizeWithinArrays(RG, method="loess", wei ...
genetics written 10.6 years ago by Jakob Hedegaard160 • updated 10.6 years ago by De-Jian ZHAO240
0
votes
0
answers
197
views
0
answers
Limma - error when using duplicateCorrelation - Windows ver. Linux
... Hi List When using duplicateCorrelation in Limma running under Linux I am receiving the following error: > cor <- duplicateCorrelation(MA, design=design, ndups=2, weights=MA$weights) Error in La.svd(QtZ, nu = mq, nv = 0) : error code 1 from Lapack routine 'dgesdd' Interestingly, there are n ...
genetics limma written 10.9 years ago by Jakob Hedegaard160
0
votes
1
answer
172
views
1
answer
Limma - plotMA3by2 & imageplot3by2 - as -pdf?
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061010/ 37c02120/attachment.pl ...
written 11.2 years ago by Jakob Hedegaard160 • updated 11.2 years ago by Jenny Drnevich2.2k
0
votes
1
answer
153
views
1
answer
Limma - error when using duplicateCorrelation
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061010/ 2aaf5d3c/attachment.pl ...
written 11.2 years ago by Jakob Hedegaard160 • updated 11.2 years ago by Gordon Smyth32k
0
votes
1
answer
195
views
1
answer
Increase in CV of replicated spots after normalization?
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050617/ 43c25640/attachment.pl ...
written 12.5 years ago by Jakob Hedegaard160 • updated 12.5 years ago by Wolfgang Huber13k
0
votes
1
answer
258
views
1
answer
SV: random block effect and technical replicates within array at the same in linear model using Limma?
... Dear Gordon & list Why is it not possible to fit random block effect and technical replicates within array in the same linear model? Is it because - the statistical theory is not ready? - or - it is not implemented in Limma? I am not a statistician so it might be a stupid question :-) Thanks ...
genetics limma written 12.5 years ago by Jakob Hedegaard160 • updated 12.5 years ago by Gordon Smyth32k

Latest awards to Jakob Hedegaard

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 2.2.0
Traffic: 327 users visited in the last hour