User: Stephane Plaisance | VIB |

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Posts by Stephane Plaisance | VIB |

<prev • 11 results • page 1 of 2 • next >
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plot multiple chromosomes from plot.type="c" to PDF files automatically in RStudio (RMD document)
... When issuing the DNAcopy command   plot(segment, plot.type="c", xmaploc=TRUE) I get in RStudio a kind of grey grid of plots of which I can click one to get the fill picture. I would like instead to get all 24 plots as separate pictures at once and have knitr convert them at knit-time to full pict ...
dnacopy written 12 days ago by Stephane Plaisance | VIB |50
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change plot title in DNAcopy multiple plot.type="s"
... I finally made it to the 24chr DNAcopy multiplot but as my chromosomes are already named chr1 ... I get plot titles like 'Chromosome chr1' which is not nice and too long to see the actual chr number. Ideally, I would like to not print 'Chromosome' Is it possible to substitute the plot titles with a ...
dnacopy written 12 days ago by Stephane Plaisance | VIB |50 • updated 12 days ago by Gavin Kelly510
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Comment: C: BiomaRT inconsistency for PDGFRA, returns FIP1L1 instead
... Dear James, Thanks very much for answering my post and very sorry that you did not get my joke about 'fraude' (of course I did not mean to be rude, just trying to put it in a funny way). Concerning your evidence that Ensembl reports a transcript spanning PDGFRA, it is nice but I kind of doubt this ...
written 13 months ago by Stephane Plaisance | VIB |50
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BiomaRT inconsistency for PDGFRA, returns FIP1L1 instead
... I try to fetch gene symbols from coordinate ranges (in good old hg19 space). It works perfectly except for one region where I get FIP1L1 in first position before the expected PDGFRA while the two genes are not even overlapping. Actually, FIP1L1 is located quite far downstream from PDGFRA. Could som ...
biomart hg19 written 13 months ago by Stephane Plaisance | VIB |50
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Answer: A: predictCoding fails with error
... Valérie, thanks so much, you are an angel. I most likely overwrote the previous unquoted with a quoted text and could never have found it myself. It is now busy running and is surely fixed. You saved my day.  Thanks you so much for the very useful package and help Stephane   ...
written 13 months ago by Stephane Plaisance | VIB |50
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Comment: A: predictCoding fails with error
... It does not seems to be my data as it also fails using package demo data (all packages already loaded as above) fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > vcft <- readVcf(fl, "hg19") > pred.coding <- predictCoding(vcft, txdb, Hsapiens) Error in (function ...
written 13 months ago by Stephane Plaisance | VIB |50
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predictCoding fails with error
... I have used the command with success many times until yesterday, I did some package updates since last success that may explain this but have no clue on what to do now. This looks like an old issue I found but does not seem to be recently reported. All my packages have been deinstalled and reinstal ...
variantannotation written 13 months ago by Stephane Plaisance | VIB |50
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Comment: C: What are the best packages to compare multiple DE gene lists?
... Thanks a lot Jose, I add RankProd to the top of my todo list! ;-) Stephane Plaisance stephane.plaisance at vib.be On 28 Aug 2014, at 10:11, Jose Garcia wrote: > Dear Stephane, > If I understood well what you need, you could use RankProd package that uses rank product non parametric a ...
written 3.2 years ago by Stephane Plaisance | VIB |50
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Comment: C: What are the best packages to compare multiple DE gene lists?
... Dear Jim, Thanks very much for this straightforward approach. I will certainly try it. My aim is to also take into account the pvalues and if applicable also the related log-FC values attached to each gene so that more than just ranking is used. I know of biotools (endeavour) that ranks lists of ap ...
written 3.2 years ago by Stephane Plaisance | VIB |50
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What are the best packages to compare multiple DE gene lists?
... I have full genome/exome lists of DE resulting from MA and/or RNASeq analyses using multiple methods (likely showing different gene even from the same samples due to technology biases). I would like to rank these lists to create a general list where redundant DE targets are pushed up and unique hits ...
written 3.2 years ago by Stephane Plaisance | VIB |50 • updated 3.2 years ago by James W. MacDonald45k

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