User: Helen Zhou

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Helen Zhou140
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140
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4 years ago
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11 years, 6 months ago
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z*********@yahoo.com

Posts by Helen Zhou

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Error when predicting features with SGSeq
... Leonard, unfortunately we have to remove temporary files due to size constraints on our folders. I will try running SGSeq next time I have some of the intermediate result file from our bioinformatics core. ~~Helen ...
written 4.1 years ago by Helen Zhou140
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Answer: A: Error when predicting features with SGSeq
... My apologize Leonard. Session info is shown below, along with the error. The bam files do contain multiple alignments. I asked our bioinformatics facility to follow the approach outlined in this G&D article, since we are also looking at neuronal stem cells. http://genesdev.cshlp.org/content/27/ ...
written 4.1 years ago by Helen Zhou140
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Error when predicting features with SGSeq
... I'm trying to use the analyzeFeatures function in SGSeq following the vignette, but I get this error: > library(SGSeq) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > sgfc <- analyzeFeatures(bam.info, which = gr) Predict features... Error in mergeTxFeatures(list_features, min_n_sampl ...
sgseq written 4.1 years ago by Helen Zhou140 • updated 4.1 years ago by Leonard Goldstein80
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Comment: C: Extract junction reads from bam
... Dear Wei and Michael, thank you both for your helpful comments. This was just what I was looking for. H Zhou On Monday, 18 August 2014, 15:35, Wei Shi wrote: Dear Helen, If you just want to get the number of reads mapping to that junction (not the actual reads), you can try featureCounts fu ...
written 5.0 years ago by Helen Zhou140
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Extract junction reads from bam
... Dear Sir/Madam, I have a bam file with reads from a paired-end RNA-seq experiments, and I would like to extract all reads that span a particular intron/exon junction. For example where part of a read maps to exon ABC starting at chr 1 position 66909348. I do not know where the first part of the rea ...
written 5.0 years ago by Helen Zhou140 • updated 5.0 years ago by Wei Shi3.1k
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p values of time serie data with timecourse package?
... Dear Sir/Madam. I seek your advice about some microarray data. I have a time serie of 6, from 0, 45m, 90m, 3h 6h and 12h. Each point has 4 replicates. I want to find diffeentially expressed genes and I am using the package timecourse. But I am not sure about the results. I run function mb.long, an ...
microarray go written 9.4 years ago by Helen Zhou140
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Comment: C: Limma time course analysis - defining comparisons
... Dear James and Others I have followed your suggestion from last week, about trying to define all contrasts in a time course analysis, and then using the nestedF option. However, I am afraid that I am still a bit confused. I run the analysis shown below, and try decideTests both with and without me ...
written 11.2 years ago by Helen Zhou140
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Answer: A: Limma time course analysis - defining comparisons
... Dear Marta, thank you for your suggestion. I am sorry it has taken me so long to reply. I have had a look at the masigpro package, but it seems to be specificaly for shorter time courses, whereas my real data set has 6 time points. Am I wrong about this? The example shown below is just because it w ...
written 11.2 years ago by Helen Zhou140
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Comment: C: Limma time course analysis - defining comparisons
... Dear Jim Thanks you for your answer. As I understand you are recommending me to do direct comparisons between for example 12-4h and 24-12h. However, could there not in theory be a gene that was up a little bit in 12vs4h and 24vs12h, so that the difference for neither of these would be large enough ...
written 11.2 years ago by Helen Zhou140
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Limma time course analysis - defining comparisons
... Dear Sir/Madam I am trying to analyse a short time series, roughly following section 8.8 in the limma user guide. I am interested in differences between all time points. I am not sure whether I have to make all the pariwise comparisons directly, or whether they can be done indirectly as well. For ...
go probe limma written 11.2 years ago by Helen Zhou140

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For Extract junction reads from bam

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