User: n.lu

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n.lu30
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Posts by n.lu

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HISAT index with ERCC
... Hi, I'd like to align my RNA-seq data from Mus musculus, containing ERCC spike-ins with HISAT2. Because I lack computer power to build my own index, I plan to downlowd a prebuilt index from their site ([ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/][1]) and as far as I can tell the only one cont ...
ercc hisat alignment rna-seq written 6 days ago by n.lu30
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Computer requirements for RNAseq alignment
... Hi, I plan on analysing the following RNA seq data: cca 30M reads/sample, 15 samples, human data. The aim is to do differential expression analysis. I plan to perform alignment with HISAT2 and I wonder if my computer (specifications below) suitable for this? - Processor: Intel(R) Core(TM) i7-47 ...
rnaseq computer alignment hisat2 written 16 months ago by n.lu30 • updated 16 months ago by genomax70k
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... Thanks, I'll check those as well. Thank you very much for your suggestions and comments!!! ...
written 22 months ago by n.lu30
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... Thanks for the explanation. I tried grouping them based on genotype (knockout vs wild type) and arthritis vs cotrol. First comparison gives 5 genes, the second none. One other thing I did was group them in two groups based on the wey they group in hierarchical clustering. The groups dont realy mak ...
written 22 months ago by n.lu30
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... Hi, thank you very much for sharing this script (and sorry for the late reply). The results are pretty much the same (same 2 genes significant, and than FDR jumps to 13% on the next one, and than to 50%). For principal components: Importance of components: ...
written 22 months ago by n.lu30
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... I didnt adjust for batch effect. PCA and clustering didnt show any gropuping by batch (half of the arrays were scanned on a different day). I also tried the algorithm for discovering unknown batches in SVA package and it foud 0 surrogate variables (although this is probably methodologicaly wrong, s ...
written 22 months ago by n.lu30
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... Limma: design <- model.matrix(~ 0+factor(c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4))) colnames(design) <- c("WT_CTRL", "WT_arthritis", "KO_CTRL", "KO_arthritis") rownames(design) <- sampleNames(eset) design WT_CTRL WT_arthritis KO_CTRL KO_arthritis WT_CTRL1 1 ...
written 22 months ago by n.lu30
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Comment: C: Almost no differentially expressed genes on microarray - what now?
... We have a knockout for a gene involved in apoptosis, and those mice dont develop experimental arthritis like wild type mice. So those were my 4 groups - wt mice control (no arthirits), wt mice with arthritis, knockout with arthritis, knockout control. wild type control vs arthritis show no differen ...
written 22 months ago by n.lu30
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Answer: A: Almost no differentially expressed genes on microarray - what now?
... Yes, synovial sample but murine synovia - cells were released from the knee joint by digestion with collagenase and myeloid (CD11b+ Gr-1+) population was sorted by FACS and used for microarray analysis. I included 14.414 genes in limma analysis. Only main probes were included, I removed those with ...
written 22 months ago by n.lu30
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Almost no differentially expressed genes on microarray - what now?
... Hi, I did my analysis on GeneChip Mouse Gene ST 2.0 Array, Affymetrix. I compared expression profiles of 4 experimental groups and got some dissapointig and surprising results). At best 2 genes are differentially expressed (limma, adjusted p 0.05 - BH correction) between groups, and none at all bet ...
no differentialy expressed genes microarray written 22 months ago by n.lu30

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Popular Question 4 months ago, created a question with more than 1,000 views. For Computer requirements for RNAseq alignment
Popular Question 14 months ago, created a question with more than 1,000 views. For Computer requirements for RNAseq alignment

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