User: Sylvain Foisy

gravatar for Sylvain Foisy
Reputation:
30
Status:
New User
Location:
Canada
Last seen:
1 year, 11 months ago
Joined:
6 years, 10 months ago
Email:
s************@inflammgen.org

Posts by Sylvain Foisy

<prev • 44 results • page 1 of 5 • next >
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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 24 months 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 24 months 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 24 months ago by Sylvain Foisy30 • updated 24 months 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 2.7 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 2.7 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 2.7 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 2.7 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 2.8 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: analyzeVariants method returns an error...
... Hi Leonard, Can do ;-) I'll work on this ASAP and let you know if it breaks/fails. Best regards S ...
written 2.8 years ago by Sylvain Foisy30
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Comment: C: Issues with SGSeq: plotFeatures method returns NULL
... Hi, Cool; that did the trick ;-) BTW and this might sound like a stupid question: how come I end up with NA values? Too low a count for SGSeq to set a value? Is there a way to fix this in analyzeFeatures, like setting a minimal value? Also another question about plotFeatures: I do see that most of ...
written 2.9 years ago by Sylvain Foisy30

Latest awards to Sylvain Foisy

Popular Question 24 months ago, created a question with more than 1,000 views. For Getting a count matrix from a SummerizedExpriment with EasyRNASeq
Popular Question 2.7 years ago, created a question with more than 1,000 views. For featureCounts simple (borderline stupid...) question
Scholar 4.8 years ago, created an answer that has been accepted. For A: Getting a count matrix from a SummerizedExpriment with EasyRNASeq

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