User: Sindre

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Sindre100
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Posts by Sindre

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Two-way interaction, linear redundancy
... Wow. That was advanced, and beautiful! I am glad this gives the same result as my approach, but I learned something new. Thank you! ...
written 11 weeks ago by Sindre100
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Two-way interaction, linear redundancy
... I want to conduct an (example) experiment. I have 3 skinny rats and 3 fat rats. First, I give them a standardized meal and will take blood samples to measure levels of protein "X" before and after this meal. Second, all rats undergoes weight loss for 1 week. Third, after weight loss, I again give th ...
limma caret lme4 lmer lm written 12 weeks ago by Sindre100 • updated 11 weeks ago by Aaron Lun25k
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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 5.4 years ago by Sindre100
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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 5.4 years ago by Sindre100
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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 5.6 years ago by Sindre100
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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 5.6 years ago by Sindre100 • updated 5.6 years ago by James W. MacDonald51k
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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 5.6 years ago by Sindre100 • updated 5.6 years ago by Yunshun Chen490
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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 5.7 years ago by Sindre100
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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 6.0 years ago by Sindre100
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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 6.0 years ago by Sindre100

Latest awards to Sindre

Popular Question 5.4 years ago, created a question with more than 1,000 views. For Labeling BAM files in Cufflinks/Cuffdiff input
Popular Question 5.4 years ago, created a question with more than 1,000 views. For edgeR: plotBCV, gof() and plotMDS, for outlier detection
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Best way of presenting "absolute" expression values (edgeR)

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