User: Sindre Lee

gravatar for Sindre Lee
Sindre Lee100
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5 years, 1 month ago
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5 years, 8 months ago
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s*********@studmed.uio.no

Posts by Sindre Lee

<prev • 10 results • page 1 of 1 • next >
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Comment: A: Best way of presenting "absolute" expression values (edgeR)
... Hi! I know a lot of people do the following: 1. Take a list of differentially expressed genes 2. Fetch the FASTA files for protein coding genes 3. Predict if secretory by using SignalP My question is, does it exist a list/database of known/predicted secretory protein coding genes from hg19? That ...
written 5.1 years ago by Sindre Lee100
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Best way of presenting "absolute" expression values (edgeR)
... Hi! We want to classify a new type of glands by ranking genes by expression level using RNAseq. We don't have any good controls, so we just want to see a ranked list of genes. I have used Cufflinks RPKM values, but if I want to use edgeR, is this a valid way of doing it using featureCounts: fc &l ...
rnaseq edger written 5.1 years ago by Sindre Lee100
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Comment: C: Filter out genes with small profile variance from gene expression data
... Hi! I have been asked to make a candidate list of genes for downstream analysis. We are going to look for secreted proteins into plasma from muscle tissue. I started by picking out genes coding for secretory proteins. Then I sorted by fold change and prediction score, but then I started wondering wh ...
written 5.3 years ago by Sindre Lee100
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Quick question about Chromosome names using Tophat2 and Cufflinks w/Ensembl NCBIM37
... Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide ...
written 5.3 years ago by Sindre Lee100 • updated 5.3 years ago by James W. MacDonald50k
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edgeR: plotBCV, gof() and plotMDS, for outlier detection
... Hello! I have been struggling with one of the skeletal muscle biopsies in my study. The RNA quality is very good and looking at tissue specific gene expression they are all there, although some with very different values for some genes compared the other biopsies. Please see the attached plots usin ...
edger written 5.3 years ago by Sindre Lee100 • updated 5.3 years ago by Yunshun Chen390
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Labeling BAM files in Cufflinks/Cuffdiff input
... Hi! I have posted this question here as well, without answer: http://seqanswers.com/forums/showthread.php?t=39978 If this is my command to Cuffdiff: cuffdiff -o path genes.gtf --labels pre,post bam1.bam,bam2.bam bam2.bam,bam3.bam The "labels" option only names the conditions, here two, "pre" and ...
written 5.4 years ago by Sindre Lee100
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edgeR with two different groups (unpaired) at two time points (paired): Need some input
... Thank you so much. If genes whose response differs in diabetic patients vs healthy = 0. Would it make any sense to "merge" the groups, thus only diabetics vs healthy or time point 1 vs time point 2, to find differences there? And also, just to be sure, is this correct? d <- (calcNormFactors(d ...
written 5.7 years ago by Sindre Lee100
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Answer: A: edgeR with two different groups (unpaired) at two time points (paired): Need som
... On 2013-10-22 20:03, Sindre Lee wrote: > Hi! > The edgeR manual is quite nice, but I'm not quite sure if I'm on the > right track.. > > The question to answer is: "Is there any significantly changed genes > in diabetics at time point 2, compared to healthy?" > > Heres my code ...
written 5.7 years ago by Sindre Lee100
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edgeR with two different groups (unpaired) at two time points (paired): Need some input
... Hi! The edgeR manual is quite nice, but I'm not quite sure if I'm on the right track.. The question to answer is: "Is there any significantly changed genes in diabetics at time point 2, compared to healthy?" Heres my codes: #Making the design matrix status <- factor(c(rep("Healthy",26), rep(" ...
edger written 5.7 years ago by Sindre Lee100 • updated 5.7 years ago by Gordon Smyth37k
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Paired data for DEseq2: Multifactorial design
... Hi! I have two groups at two time points. And the samples are the same in both time points. I have run this in DESeq2: sampleFiles <- list.files(path="/Volumes/timemachine/HTseq_DEseq2",pattern="*.txt"); status <- factor(c(rep("Healthy",26), rep("Diabetic",22))) timepoints = as.factor(c(1,1,1 ...
limma written 5.7 years ago by Sindre Lee100 • updated 5.7 years ago by Michael Love24k

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