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Guest User12k
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Posts by Guest User

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positively correlated genes
... hi I am interested to find out the genes that are positively and negatively correlated genes with my genes of interest. (using rnaseq normalized expression data). Can some one suggest me a better option. Thank you -- output of sessionInfo(): sessionInfo() R version 3.0.2 (2013-09-25) Platfor ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by Gordon Smyth32k
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Converting .gpr files to .csv files
... I just got some microarray data sent over to me. The files are .gpr and I would like to convert then to .csv files to open the data in excel and eventually in R. Im not sure how to go about doing that. -- output of sessionInfo(): R version 3.1.1 (2014-07-10) Platform: i386-w64-mingw32/i386 (32-bi ...
microarray go convert written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k
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Test Statistic in nbinomialTest in DESeq???
... Hi everyone, Does nbinomialTest in DESeq calculate a test statistic? According to DESeq documentation, "nbinomTest calculates a p value by summing up the probabilities of all per-group count sums a and b that sum up to the observed count sum kiS and are more extreme than the observed count sums kiA ...
deseq written 3.2 years ago by Guest User12k • updated 3.2 years ago by Wolfgang Huber13k
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HTSeq-Count
... Hi all, I am new to the field of seq and performed a RIP-Seq experiment using HTSeq count as counter. I get now the following (using union, but doesn??t look better for interesection_strict): __no_feature 1503377 __ambiguous 490772 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 5 ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by Yuan Hao240
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virtualArray package
... Hi, I am very interested in using the virtual array package and have been trying it out. However, i have been getting this error (see below) even with the test data in the paper. Could you kindly advise please? -- output of sessionInfo(): > my_virtualArrays$iPSC_hESC_noBatchEffect <- vi ...
annotation preprocessing hgu133plus2 hgug4112a written 3.2 years ago by Guest User12k
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MEDIPS: how does MEDIPS define a methylated region / cluster?
... Hi, I have aligned my sequencing data for one sample (filename: Ca2_MAPQ20.bam --- because I filtered out everything with MAPQ20 or less) and I've put it through MEDIPS. At the moment, I am not making a comparison between samples. Therefore, the result file shows the methylation profile for only one ...
sequencing medips written 3.2 years ago by Guest User12k • updated 3.1 years ago by mengru12230
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SAM analysis of two color microarray data
... Dear Biconductor, I am new to analysis of micro array data and I am trying to analyse a two colour micro array data. I was trying to reproduce the results in the paper (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-120/ ). In this paper, the authors say that they have normalized the data us ...
normalization limma siggenes written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k
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GWASTools: quasi-/perfect linear separation
... This is not really a question but more of a warning to other users. I have performed a regression analysis using the assocTestRegression function under three different models (dominant,recessive,additive). My data set contains ~3 million markers which have been filtered so that only SNPs with >= ...
regression written 3.2 years ago by Guest User12k • updated 3.2 years ago by Stephanie M. Gogarten530
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edgeR factorial experiment contrasts
... Hi, I am trying to figure out how to do comparisons using edgeR but have to admit that I am on unsure ice. My experiment is abiotic stress on two genotypes (E and J) and these have been sampled for RNA-seq at five time points (00, 01, 05, 48, and 96). I would like to analyze this experiment as a fac ...
edger written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k
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edgeR contrast
... I try different contrasts with edgeR to get a feeling for my data and also to find out the best contrast for my question. I would like to know what genes are enriched in IP.treat compared to IP.control, both adjusted for unspecific IgG binding. So it seems like contrast 1 is the best: (IP.treat-IgG. ...
edger written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k

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Oracle 3.2 years ago, created more than 1,000 posts (questions + answers + comments).
Popular Question 3.2 years ago, created a question with more than 1,000 views. For no method for coercing S4 class to a vector
Popular Question 3.2 years ago, created a question with more than 1,000 views. For no method for coercing S4 class to a vector
Popular Question 3.2 years ago, created a question with more than 1,000 views. For no method for coercing S4 class to a vector
Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq - plotPCA
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Popular Question 3.2 years ago, created a question with more than 1,000 views. For virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Popular Question 3.2 years ago, created a question with more than 1,000 views. For virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq - plotPCA
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Installation of SomaticSignatures
Popular Question 3.2 years ago, created a question with more than 1,000 views. For R 2.15.2 trouble
Popular Question 3.2 years ago, created a question with more than 1,000 views. For no method for coercing S4 class to a vector
Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq2(analysis without replicate)
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