## User: A

A40
Reputation:
40
Status:
New User
Location:
Last seen:
2 weeks, 5 days ago
Joined:
2 years, 1 month ago
Email:
a***********@gmail.com

#### Posts by A

<prev • 76 results • page 1 of 8 • next >
1
118
views
1
... 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 9 weeks ago by A40
1
118
views
1
... 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 10 weeks ago by A40
1
118
views
1
... 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 ...
written 10 weeks ago by A40 • updated 10 weeks ago by swbarnes2340
0
83
views
0
... 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 10 weeks ago by A40
0
83
views
0
... Brilliant! thank you so much! i will proceed like this! The code above for generating the new counts matrix is ok? thanks! ...
written 10 weeks ago by A40
0
83
views
0
... 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 10 weeks ago by A40
0
83
views
0
... 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 ...
written 10 weeks ago by A40
1
161
views
1
... 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 10 months ago by A40
1
161
views
1
... 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 ...
written 10 months ago by A40 • updated 10 months ago by James W. MacDonald52k
1
234
views
1
... 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 10 months ago by A40

#### Latest awards to A

Teacher 11 months ago, created an answer with at least 3 up-votes. For C: RSubread in cygwin

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.