User: Sylvain Foisy

gravatar for Sylvain Foisy
Reputation:
30
Status:
New User
Location:
Canada
Last seen:
2 months, 1 week ago
Joined:
7 years, 1 month ago
Email:
s************@inflammgen.org

Posts by Sylvain Foisy

<prev • 46 results • page 1 of 5 • next >
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Comment: C: SGSeq: core dumped after running convertToSGFeatures() method
... Hi, This happen every time I try to use SGSeq on this particular system; that has not happen to me on my previous work system, my own laptop or my personal server. My guess is a strange/toxic interaction between SGSeq and this local R install but I need to be sure before I start bugging the sysad ...
written 10 weeks ago by Sylvain Foisy30
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SGSeq: core dumped after running convertToSGFeatures() method
... Hi, I perviously used SGSeq on our own server w/o any issue; however, we moved our analysis pipeline to a shared facility and I have been unable to more forward using my previously-working pipeline. Here is my R commands, more or less lifted from the docs: # loading my sample list load.d & ...
sgseq coredump written 10 weeks ago by Sylvain Foisy30
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Comment: C: SGSeq: moving toward diffex from SGSeq analysis
... Hi Leonard, Thanks for the info; I'll be playing some more and if needed, may be bug you again ;-) Best regards S ...
written 2.2 years ago by Sylvain Foisy30
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Comment: C: SGSeq: moving toward diffex from SGSeq analysis
... Hi Leonard, No problem ;-) Ok, as per section 11, I created objects for counts, exon ID and gene ID with the methods in the vignette: # My R stuff: # sgfc.denovo.var is my equivalent to sgvc_pred > sgv.ranges<-rowRanges(sgfc.denovo.var) > sgv.counts<-getSGVariantCounts(sgv.ranges,samp ...
written 2.2 years ago by Sylvain Foisy30
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SGSeq: moving toward diffex from SGSeq analysis
... Hi, I have use SGSeq mostly to look at exon usage for genes of interest in my RNASeq datasets. I would like to move toward exon diffex analysis. I followed the recipes in the HTML guide to get counts, exons and gene ID but I am perplexed about what I got... I have an SGFeatureCounts object with cre ...
rnaseq sgseq written 2.2 years ago by Sylvain Foisy30 • updated 2.2 years ago by Leonard Goldstein80
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi, Another issue that I am getting: when running plotFeatures() for a specific gene, I have this: > plotFeatures(sgfc.denovo,geneName="TMEM56-RWDD3",color_novel="red",include="both") Error in strsplit(co, split = ":", fixed = TRUE) : non-character argument Any idea on cause? I want to create ...
written 3.0 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi Leonard, I kind of knew that it needed matching row and assays; my problem is that I have matching assays but a quick look at the rows cashes much differences... I'll have to find a way of putting missing rows in reciprocating sets with 0 values for missing info. Thanks again for your help S ...
written 3.0 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi Leonard, Cool, can do. I'll keep you posted but it might take a while.. Yo are right that these datasets are both genome-wide and multi-samples; I have n=8 to n=12 for each... BTE, and possible on a different tangent from the original question: let's say that I have done my analysis per cell typ ...
written 3.0 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi Leonard, Sorry for the long delays: I reach and I admin and my analysis time has been short this fall... Ok, I installed the latest SGSeq and I got a new type of errors :-( Trying to do my analysis pipeline, it failed while doing analyzeFeatures() with annotation file with this after computing f ...
written 3.0 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi, Actually, NA was used only in my first tries; I played with the numbers a bit since then. Thanks for the inputs! S ...
written 3.1 years ago by Sylvain Foisy30

Latest awards to Sylvain Foisy

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Getting a count matrix from a SummerizedExpriment with EasyRNASeq
Popular Question 2.9 years ago, created a question with more than 1,000 views. For featureCounts simple (borderline stupid...) question
Scholar 5.1 years ago, created an answer that has been accepted. For A: Getting a count matrix from a SummerizedExpriment with EasyRNASeq

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