User: carl.h

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carl.h10
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Posts by carl.h

<prev • 20 results • page 2 of 2 • next >
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Comment: C: How to visualize gene difference with PCA?
... Thank you for the answer, and if I am not that precise in my explanation, that is because I am a beginner in analyzing RNA-seq data. As I understand it the PCA data from prcomp() have the positions of the samples and also the vector directions of the genes. I have tried printing a biplot with both v ...
written 3.1 years ago by carl.h10
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How to visualize gene difference with PCA?
... I am trying to visualize the gene expression difference between different samples. I am using edgeR to analyze rna-seq data. I have done PCA and MDS plots on the samples and the samples separate nicely into groups between treatments and time points. Now I would like to see how the genes separate on ...
rna-seq written 3.1 years ago by carl.h10
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Comment: C: How should I construct this contrast?
... I am sorry, but I am still not sure how I would construct the contrast. For example If I would like to show which genes are up regulated in KOTGF treated compared to WTTGF. ...
written 3.1 years ago by carl.h10
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How should I construct this contrast?
... I want to study the effect of TGF-beta between two genotypes WT and KO. To compare the two genotypes, we have knocked out (KO) the gene using the parental as WT control. Then we have stimulated the cells with TGF-beta at 1 hour and 24 hours. I created a design matrix for comparing the groups that l ...
rna-seq edger written 3.1 years ago by carl.h10 • updated 3.1 years ago by mforde841.2k
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Comment: C: How can I count one specific exon in RNA-seq data
... Thank you it worked perfectly, I had to add -f to count feature. ...
written 3.1 years ago by carl.h10
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Comment: C: How can I count one specific exon in RNA-seq data
... For a follow up question, you don't happen to know how to count all exones in one gene? I have the gtf annotations for all the exones in one gene and I would like to get the number of each exon for the gene. ...
written 3.1 years ago by carl.h10
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Comment: C: How can I count one specific exon in RNA-seq data
... Yes that is right. Thank you! ...
written 3.1 years ago by carl.h10
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How can I count one specific exon in RNA-seq data
... I would like to quantify the number of exones of one particular exone in a specific gene. I have rnaseq data. ...
rna-seq written 3.1 years ago by carl.h10 • updated 3.1 years ago by Charles Warden7.6k
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Looking at treatment effects with contrasts multiple groups
... I am trying to study the effect of TGF-beta between two genotypes WT and KO in MEF cells. To compare the two genotypes, we have knocked out (KO) the gene using the parental as WT control. Then we have stimulated the cells with either TGF-beta or just serum free control, these cells we have analysed ...
rna-seq edger written 3.2 years ago by carl.h10
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Constructing design matrix for batch effect, without intercept.
... I am figuring out to how construct a design matrix for a multi variate experiment. I am using edgeR to analyse the gene expression data of 32 different samples. There are 16 gene knock-outs (KO) and16 wildtype controls (WT). The experiment is constructed with two time points ( 1h and 24h) and with ...
design matrix rna-seq edger written 3.2 years ago by carl.h10

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