User: Boel Brynedal

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Boel Brynedal200
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Posts by Boel Brynedal

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Comment: C: HGNC annotation for use in GOstats
... Hi Jim, Worked like a charm. Thanks! 10 dec 2013 kl. 15:33 skrev James W. MacDonald : > Hi Boel, > > On Tuesday, December 10, 2013 5:02:50 AM, Boel Brynedal wrote: >> >> Dear All, >> >> I am attempting a fairly simple thing: performing a hypergeometric test for ge ...
written 5.5 years ago by Boel Brynedal200
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HGNC annotation for use in GOstats
... Dear All, I am attempting a fairly simple thing: performing a hypergeometric test for gene sets using GOstats. My gene set is in HGNC symbols as is my 'gene universe? vector. But GOstats seems to require entrez IDs. Could anyone point me to a hgnc annotation package that includes entrez IDs? Or an ...
annotation gostats written 5.5 years ago by Boel Brynedal200 • updated 5.5 years ago by James W. MacDonald50k
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Comment: C: Genominator error when calling syste.time
... Changing to very vanilla names in the sample vector and actually giving the chroms vector (...) solved the problem. Thanks! ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com] Sent: Thursday, April 12, 2012 11:45 AM To: Boel Brynedal Cc: Dan Tenenbaum; ...
written 7.1 years ago by Boel Brynedal200
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Comment: C: Genominator error when calling syste.time
... I have 12 GB of RAM for this job, and the BAM files are not particularly big. Is it likely that this is a memory issue? I'm writing the files in my own folder on a larger cluster, so there should not be a problem with permissions. Or? How can I investigate whether this is a permission issue? Changi ...
written 7.1 years ago by Boel Brynedal200
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Genominator error when calling syste.time
... Hi All, I am analyzing some ChIP seq data using DESeq, reads have all been aligned and are in BAM format. "aligned" in a names character vector containing the names of the bam files. I'm trying to use the Genominator function importFromAlignedReads to read in the aligned data, but I get an error re ...
genominator deseq written 7.1 years ago by Boel Brynedal200 • updated 7.1 years ago by Kasper Daniel Hansen6.4k
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Retrieving gene name where given genomic region is included.
... Dear List, I have long lists of genomic regions (chr;start;end) where a given event has taken place. These regions can be an exon, an intronic region, or similar. Most (all) of these events have taken place within the boundaries of genes, and I would like to retrieve the gene names (ensemble ID). ...
written 9.4 years ago by Boel Brynedal200 • updated 9.3 years ago by Steve Lianoglou12k
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Link to picture: Comparison of diff. t-statistics, Limma and rowttests
... Dear List, I suddenly understood that had happened and just thought I would let you know. ordinary.t has two columns; > ordinary.t[1:3,] (Intercept) specificstageA 117_at 34.92382 1.7682627 1552264_a_at 39.52028 -1.5384353 1552277_a_at 23.21122 -1.6098082 ...
hgu133plus2 affy limma gcrma written 10.8 years ago by Boel Brynedal200
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Link to picture: Comparison of diff. t-statistics, Limma and rowttests
... Hi, again, Just a small note, the "fit3" in ordinary.t is simply a error from my side. It should be: ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma This does not change the way ordinary.t behaves. Best, Boel Thank you Al. > > > -----Original Message----- > > From: bioc ...
hgu133plus2 affy limma gcrma written 10.8 years ago by Boel Brynedal200
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Answer: A: Comparison of diff. t-statistics, Limma and rowttests
... Dear List, Thank you (Wolfgang and Paolo) for telling me the attachment did not get through. This is a link to the picture: http://picasaweb.google.se/Boelbubblan/Statistics/photo Cheers, Boel --~*~**~***~*~***~**~*~-- Boel Brynedal, MSc, PhD student Karolinska Institutet Department of Clinical ...
written 10.8 years ago by Boel Brynedal200
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Comparison of diff. t-statistics, Limma and rowttests
... Dear List, I have affy hgu133plus2 arrays from individuals with disease, in two different stages of the disease. I've earlier used rowttests and FDR correction. Now I was playing around with limma to see what I could do (added different covariates etc) but also investigated the most simple setting, ...
hgu133plus2 affy limma gcrma written 10.8 years ago by Boel Brynedal200

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