User: hakimelakhrass

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Posts by hakimelakhrass

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Really weird results when I filter this new data that I have, script has worked on two previous data sets.
... So this is my script and I have used it in the past. The filtering and then getting my list of DEG. The list contains only pos_controls from affymetrix but no main probes. Which I do not understand because I thought I removed them with the filter step which works on my other 2 datasets. Thanks! my ...
microarray genefilter limma written 2.4 years ago by hakimelakhrass0 • updated 2.4 years ago by James W. MacDonald46k
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nsFilter not filtering out all of the normgene->exon.
... Hello, I am trying to only use genes labeled as main. So i tried to filter all but main including the normgene but it did not work. con <- db(pd.hugene.2.0.st) probes.control <- dbGetQuery(con, "select fsetid from featureSet where type in ('3', '5','6','7','8 ...
genefilter affymetrix microarrays written 2.4 years ago by hakimelakhrass0 • updated 2.4 years ago by James W. MacDonald46k
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... I apologize for the improper use of the forum and will take note for future posts. I actually have a pretty big background in statistics but was just having problems applying it to this type of data. In the future I will only post about technical issues. ...
written 2.4 years ago by hakimelakhrass0
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... Unfortunately I am a total noob and don't even know what type of test I should be doing. ...
written 2.4 years ago by hakimelakhrass0
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... but also as far as the control goes. that is what i thought the design should be following the limma documentation. I must have misunderstood. If you can point me in the right direction as a way to continue the DE analysis that would be greatly appreciated. ...
written 2.4 years ago by hakimelakhrass0
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... but also as far as the control goes. that is what i thought the design should be following the limma documentation. I must have misunderstood. ...
written 2.4 years ago by hakimelakhrass0
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... Okay, I think I understand. My volcano plot is now fixed. I think I am going in the right direction. Thank you! ...
written 2.4 years ago by hakimelakhrass0
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Comment: C: Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... The script works, I should have worded that differently. I am the one who doesn't understand so well the output of my script.  My first question is if it is possible to use the limma package with dependent data (time series). If so then this script may be alright; I still do not understand my outpu ...
written 2.4 years ago by hakimelakhrass0
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Still need help identifying a good workflow for finding DEG in hugene 2.0 st
... Hi everyone, I am new to microarray data and I am having a really hard time finding a good work flow so far. My experiment is with human transcriptome data. I have 4 time points and I am trying to find DEG between them. This is just a test run with two times points. I have no idea what to do and so ...
microarray limma oligo hugene20 written 2.4 years ago by hakimelakhrass0 • updated 2.4 years ago by Aaron Lun20k
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DE analysis pipeline with Hugene 2.0 ST arrays
... Hello So I finally fixed some problems I was having with R in intial processing and now have questions of the workflow/pipeline for DE analysis for semitime series dataset in limma. My experiment is trying to find the DE genes between 4 different time points. The reason I say semi time series is be ...

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