User: Natasha

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Natasha0
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Posts by Natasha

<prev • 28 results • page 2 of 3 • next >
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Comment: C: Downloading microarray data for DEG analysis!
... That makes it very clear, thank you! appreciate it. ...
written 15 days ago by Natasha0
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Comment: C: Best DEG tool for datasets with FPKM counts?
... Thank you for the information. ...
written 15 days ago by Natasha0
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Answer: A: Best DEG tool for datasets with FPKM counts?
... Hi Steve, Thank you so much for your reply. When I do sample(dat$gebe_id, 20), I get this:  [1] Acot8         Tarm1         Aph1b          [4] Cga           Ptms          Irx3           [7] 1700003F12Rik Six3          Tdh           [10] Olfr67        Gm14327       Stx6          [13] Zfp868        ...
written 16 days ago by Natasha0
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Best DEG tool for datasets with FPKM counts?
... Hi everyone, I have a dataset that contains FPKM values for 5 samples. Is it alright to carry out log2 transformation on these values and using Limma on them or is there a better way to do this? Also, my gene_id column contains something like this- 0610005C13Rik,  0610007L01Rik. Could anyone guide ...
fpkm written 16 days ago by Natasha0
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Comment: C: Downloading microarray data for DEG analysis!
... Hi James, Thank you for your reply. I went through ?annotateEset and have a few questions that I hope are not too basic. 1) Firstly, what would be the difference between mogene10strranscriptcluster.db and pd.mogebe.1.0.st.v1? And how would I know to look for these packages within the library "affy ...
written 16 days ago by Natasha0
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Comment: C: Downloading microarray data for DEG analysis!
... Hi James, If I could just extend this question- I have another dataset that contains microarray data and the GEO platform mentioned is [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. I am not sure if that was useful information but I used the before mentioned  protoc ...
written 18 days ago by Natasha0
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Comment: C: Downloading microarray data for DEG analysis!
... This was extremely informative and makes my understanding a lot clearer. I used the code you provided and it worked perfectly. Thanks so much, appreciate it James! ...
written 19 days ago by Natasha0
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Downloading microarray data for DEG analysis!
... Hello, I am currently following this protocol:  https://www.bioconductor.org/packages//2.7/bioc/vignettes/oligo/inst/doc/V5ExonGene.pdf to download Microarray data from GEO.  Firstly, when I try the command for rma analysis, I see this error. > genePS <- rma(affyGeneFS, target="probeset") ...
affymetrix microarrays written 19 days ago by Natasha0 • updated 19 days ago by James W. MacDonald45k
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Comment: C: Creating design and contrast matrices for DEG with Limma for 2 factors?
... Thank you, I shall look up ?topTable. ...
written 20 days ago by Natasha0
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Comment: C: Creating design and contrast matrices for DEG with Limma for 2 factors?
... Hello Aaron, Thank you so much for your reply. Section 9.5 of the user  guide was very useful indeed. However, I am a little confused about what this means in the guide. "A list of top genes for RNA2 versus RNA1 can be obtained from > topTable(fit2, coef=1, adjust="BH") " Here, since sort.by ...
written 20 days ago by Natasha0

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