User: A

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A40
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Comment: C: Batch effects between different sequencing runs
... Many thanks all!! appreciate the response and clarification... this indeed makes perfect sense.. a quick few follow up questions: With this as a caveat: is it ok to simply proceed with `~Group` in the model , to model differences between the difference conditions (groups)? And secondly, in the cas ...
written 8 days ago by A40
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Comment: C: Batch effects between different sequencing runs
... thank you! SampleName Organism Replicate Group SequenceRun Molecule C11orf95_R1 EV_R1 Mus musculus 1 empty vector control 1 RNA C11orf95_R2 EV_R2 Mus musculus 2 empty vector control 1 RNA C11orf95_R3 EV_R3 Mus musculus 3 empty vect ...
written 9 days ago by A40
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Batch effects between different sequencing runs
... Hi all, I would be really greatful if somebody could provide some insight about how to go about comparing two experiments that have both been sequenced at different times (and potentially in a different manner (for example single end vs paired end). I am trying to model the batch effect in DESeq2 ...
deseq2 batchcorrection written 9 days ago by A40 • updated 9 days ago by swbarnes2330
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Comment: C: Extracting VST matrix with batch effects removed
... you did, apologies, i wasn't sure if yes was referring to the whole statement or the interpretation about mean shift removal! thanks again! ...
written 11 days ago by A40
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Comment: C: Extracting VST matrix with batch effects removed
... Brilliant! thank you so much! i will proceed like this! The code above for generating the new counts matrix is ok? thanks! ...
written 11 days ago by A40
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Comment: C: Extracting VST matrix with batch effects removed
... Thank you! so by running `removeBatchEffect` in limma, the mean shifts are removed in the same way they would be when including batch in the reduced model? is this a correct interpretation of Michaels comment? so then, would: newCounts<-removeBatchEffect(assay(vsd), vsd$Extraction)) wr ...
written 11 days ago by A40
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Extracting VST matrix with batch effects removed
... Hi all, Was just wondering if somebody would be able to clarify something for me regarding variance stabilising transformation and batch correction and subsequently extracting a matrix of batch corrected VST counts. I have run an experiment as follows: DESeqDataSetFromMatrix(countData = cou ...
deseq2 batchcorrection written 11 days ago by A40
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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 8 months ago by A40
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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 8 months ago by A40 • updated 8 months ago by James W. MacDonald51k
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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 8 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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