User: Fabrice Tourre

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Posts by Fabrice Tourre

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How to get gene symbol after deseq?
... Dear experts, After I have run deseq, I got a list of genes. They are something like as follow. > resSig[,1] [1] "ENSMUSG00000022150+ENSMUSG00000079102:009" [2] "ENSMUSG00000026727:016" [3] "ENSMUSG00000026727:004" [4] "ENSMUSG00000022150+ENSMUSG00000079102:015" [5] "ENSMUSG00000025730:010" [6] ...
deseq written 5.5 years ago by Fabrice Tourre970 • updated 5.5 years ago by James W. MacDonald50k
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Comment: C: DEXseq error on estimatelog2FoldChanges
... Because the deep sequencing experiment is very expensive (at least to some not so rich labs), we cannot do a biological replication. We try to find some hints through RNA-seq, then do benchmark experiment to valid the sequencing results. On Tue, Feb 4, 2014 at 9:23 AM, Fabrice Tourre wrote: > ...
written 5.6 years ago by Fabrice Tourre970
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Comment: C: DEXseq error on estimatelog2FoldChanges
... Alejandro, Thank you very much. Yes. I have only one control and one knockdown, without replication. Do you have any suggestions how can I get the differences in exon in two condition. Or different alternative splicing in two different condition. DESeq2 can do this? On Tue, Feb 4, 2014 at 9:18 AM, ...
written 5.6 years ago by Fabrice Tourre970
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Comment: C: DEXseq error on estimatelog2FoldChanges
... I am analyzing mouse samples. > any( duplicated( paste( geneIDs(ecs), exonIDs(ecs), sep=":") ) ) [1] FALSE > any( duplicated( featureNames(ecs)) ) [1] FALSE > design(ecs) countFile ~/projects/seqdata/data/tophat2/sample1/sample1.counts ~/projects/seqdata ...
written 5.6 years ago by Fabrice Tourre970
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Answer: A: DEXseq error on estimatelog2FoldChanges
... Dear expert, When I use DEXSeq to find different expressed exon, I got this error. In my analysis, I only have two samples, one is case, one is control. ecs <- estimatelog2FoldChanges( ecs ) Error in `row.names<-.data.frame`(`*tmp*`, value = c("geneID", "exonID", : duplicate 'row.names' a ...
written 5.6 years ago by Fabrice Tourre970
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DEXseq error on estimatelog2FoldChanges
... Dear expert, When I use DEXSeq to find different expressed exon, I got this error. In my analysis, I only have two samples, one is case, one is control. ecs <- estimatelog2FoldChanges( ecs ) Error in `row.names<-.data.frame`(`*tmp*`, value = c("geneID", "exonID", : duplicate 'row.names' a ...
dexseq written 5.6 years ago by Fabrice Tourre970
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Comment: C: kmer and zscore calculation
... Thank you very much. It is helpful. On Thu, Dec 19, 2013 at 1:33 PM, Hervé Pagès wrote: > [Oops, forgot to Cc the list when I answered this. Sending it again...] > > > Hi Fabrice, > > The oligonucleotideFrequency() function in the Biostrings > package counts the nb of occurren ...
written 5.7 years ago by Fabrice Tourre970
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Comment: C: kmer and zscore calculation
... Julian, Thank you for your reply. For example, I have a sample fastq file. >chr1:14404-14435(-) GGCACA >chr1:14409-14440(-) AAAACG >chr1:14423-14454(-) AGAGGC >chr1:14424-14455(-) AAGAGG I want to calculate 6kmers in this sample file. Also I have extract a control fastq file. >ch ...
written 5.7 years ago by Fabrice Tourre970
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Comment: C: kmer and zscore calculation
... Julian, Thank you for your reply. For example, I have a sample fastq file. >chr1:14404-14435(-) GGCACA >chr1:14409-14440(-) AAAACG >chr1:14423-14454(-) AGAGGC >chr1:14424-14455(-) AAGAGG I want to calculate 6kmers in this sample file. Also I have extract a control fastq file. >ch ...
written 5.7 years ago by Fabrice Tourre970
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kmer and zscore calculation
... Dear list, I have a list of bed regions. each region is 10bp length. I want to calculate the hexamers and pentamers in theses regions and get the zscore. Is there any existed packages to do this? Thank you very much in advance. ...
written 5.7 years ago by Fabrice Tourre970 • updated 5.7 years ago by Hervé Pagès ♦♦ 14k

Latest awards to Fabrice Tourre

Popular Question 5.0 years ago, created a question with more than 1,000 views. For deseq2: convert ensembl ID to gene symbol.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For From location to get the SNP rs ID
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Deseq2 for down stream analysis
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Get all 3'utr and 5'utr region from GenomicFeatures
Popular Question 5.0 years ago, created a question with more than 1,000 views. For GO terms: Annotation for HumanMethylation450
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Using Biostring to make position frequency matrix
Popular Question 5.0 years ago, created a question with more than 1,000 views. For From location to get the SNP rs ID
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Fast way to find which gene a snp located.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For sva remove batch effect.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For kmer and zscore calculation
Popular Question 5.0 years ago, created a question with more than 1,000 views. For From location to get the SNP rs ID
Popular Question 5.0 years ago, created a question with more than 1,000 views. For PCA to remove batch effect.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Calculate coverage on genome.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How to get the all CpG sites genome postion for mm9?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How to output Normalised count data from DESeq?
Great Question 5.0 years ago, created a question with more than 5,000 views. For deseq2: convert ensembl ID to gene symbol.

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