User: chris86

gravatar for chris86
chris86340
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Location:
UCL, United Kingdom
Last seen:
10 hours ago
Joined:
2 years, 7 months ago
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 146 results • page 1 of 15 • next >
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CAMERA fold changes per gene set?
... Dear bioconductor/ limma developers I was wondering if there is a straightforward way of getting fold changes per gene set out when I run CAMERA or any of the gene set functions in limma. This is because I need to plot them. I am enjoying using the general pipeline, but at the moment to get the fol ...
limma written 5 weeks ago by chris86340
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Comment: C: Paired factorial design model in limma
... Thanks Aaron ...
written 9 weeks ago by chris86340
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Paired factorial design model in limma
... Hi I have three pathotypes any single patient may belong to at baseline, then I have two timepoints for each patient, baseline and six-month. I am interested in what changes within a pathotype from baseline to six-months, i.e. a paired comparison. Then, I am also interested in what is different bet ...
limma written 10 weeks ago by chris86340 • updated 10 weeks ago by Aaron Lun18k
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Comment: C: apply Kruskall or other non-parametric test for multiple comparisons
... I'd just use limma or one of the other bioconductor packages like DESEQ2. ...
written 11 weeks ago by chris86340
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Comment: C: apply Kruskall or other non-parametric test for multiple comparisons
... Why do you want a non-parametric test? ...
written 11 weeks ago by chris86340
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Comment: C: Probe summerization of Human HT-12 V4 BeadChip arrays
... I can only say I use limma code for importing and normalising this type of array and then use the limma avereps function to average to genes, it is easy, I never got on well with beadarray for some reason. ...
written 3 months ago by chris86340
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Answer: C: Normalize depth before calculating TPM
... TPM is for comparing expression strength of different genes, this is what you want. The DESEQ normalisation method is for doing differential expression between groups, not comparing expression strength. I'd just take the mean for the replicates, but the median is reasonable. ...
written 3 months ago by chris86340
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Comment: C: Differential expression between multiple groups
... Do you mean you want to do an ANOVA? Limma does this. ...
written 3 months ago by chris86340
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Answer: C: Using tximport to convert a dataframe consisting of tpm to counts for use with l
... You wouldn't use tximport to convert a matrix of TPM counts into CPM. The question of using TPMs for differential expression with limma has been covered before here: https://support.bioconductor.org/p/98820/ ...
written 3 months ago by chris86340
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Comment: C: Diferential expresion analysis between different microarray platforms
... I don't think you should do that. ...
written 3 months ago by chris86340

Latest awards to chris86

Popular Question 8 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 22 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Centurion 22 months ago, created 100 posts.
Scholar 22 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 22 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 22 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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