User: A

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A40
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Posts by A

<prev • 76 results • page 2 of 8 • next >
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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 8 months ago by A40 • updated 8 months ago by Martin Morgan ♦♦ 23k
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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 9 months ago by A40
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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 9 months ago by A40 • updated 9 months ago by Michael Love25k
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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 9 months ago by A40
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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 9 months ago by A40
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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 9 months ago by A40
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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 9 months ago by A40
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... Hi Wei,  Resurrecting this post! I figured out the problem and it was simply the sequence of the FASTA file. It was incorrect and the sequence in the cloning vector was slightly different to the reporter gene on the embl website. I am trying to annotate this and generate counts using featurecounts ...
written 9 months ago by A40
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... Ok thank you! Yes I am trying to manually blast the sequence to see if its there! ...
written 10 months ago by A40
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Comment: C: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
... Thank you!! ...
written 10 months ago by A40

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Teacher 9 months ago, created an answer with at least 3 up-votes. For C: RSubread in cygwin

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