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User: A

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A • 40
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Posts by A

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Comment: C: Creating a similarity matrix for genes and not values
... Thanks! I will do that next time!.. With regards to your proposed solution, the frequency of the individual genes themselves isn't helpful in understanding groups of genes that are associated with reference genes throughout. Its about how many other genes it occurs with.So while its useful to know ...
written 12 days ago by A • 40
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Creating a similarity matrix for genes and not values
... Hi all, I was wondering if anybody might have some advice on identifying groups of genes that occur in groups multiple times in a list. I am carrying out time series data analysis and i carried out a co-expression analysis which is really nice, giving us nice ideas of which genes might be changin ...
similarity matrix common genes recurring groups written 12 days ago by A • 40 • updated 12 days ago by James W. MacDonald ♦ 49k
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Comment: C: Results table completely wrong for specified contrast of
... Thank you so so much for confirming and for clarifying this. No further questions! I can now analyse the data! Thank yo for your time :) ...
written 26 days ago by A • 40
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Comment: C: Results table completely wrong for specified contrast of
... Thank you so much for that clarification and the link, that is perfectly clear! With regards to your second question.. This is a developmental time course experiment across different genotypes. However as well simpyl doing a time series analyses, we would also like to carry out pairwise comparisons ...
written 26 days ago by A • 40 • updated 26 days ago by Martin Morgan ♦♦ 22k
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Comment: C: Results table completely wrong for specified contrast of
... Thank you for clarifying! So just so I'm clear .. is this 1.2 fold increase in the first contrast though? So 1.2 fold increased in the normal sample vs knockout? Secondly, when specifying a contrast if the same age group, would this not mitigate the effects of age specified in the contrast as thes ...
written 29 days ago by A • 40
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Results table completely wrong for specified contrast of
... Hi all, I was wondering if anybody has experienced this issue or if someone can chime in on a very frustrating problem I am having. I think I have not specified my groups correctly given the count data and just the fact that with normalized counts I am getting completely different log fold changes ...
deseq2 counts logfoldchange written 29 days ago by A • 40 • updated 29 days ago by Michael Love ♦ 22k
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Comment: C: RSubread in cygwin
... aaaa sorry!! Never posted an answer on this forum (as mainly ever asked questions ha!) Is there a way to change this? Many thanks! ...
written 5 weeks ago by A • 40
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Answer: C: RSubread in cygwin
... If you download R from cygwin, you can then download subread through bioconductor on the R package running on cygwin... once R is installed, type R, enter and you'll have R up and running. install rsubread through bioconductor as you would normally I also found the linux shell downloadable from the ...
written 5 weeks ago by A • 40
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Data preparation and Machine learning on time course RNAseq data
... Hi all, I was wondering if anybody is familiar with machine learning techniques and RNAseq data. I have time-course RNA seq data from multiple different samples, i.e, organs. What I would like to do is extract patterns that are forming in the data going from time 0 up to the last time point. How ...
rnaseq mlseq machine learning deep learning written 6 weeks ago by A • 40
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... UPDATE Fixed! Top line of the FASTA file was ZsGreen1       (696 bp),  I thought 696bp was part of the title, but changing the first line to ZsGreen1 alone solved the problem!!   ...
written 8 weeks ago by A • 40

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