User: RNAseqer
RNAseqer • 110
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- 110
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- Last seen:
- 1 week, 2 days ago
- Joined:
- 5 months, 1 week ago
- Email:
- z*****@gmail.com
Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.
Posts by RNAseqer
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... I'm fairly new to limma and just want to double check if I am doing something correctly. I have some microarray data and am looking for genes differentially expressed between states DIS and TE. I have several continuous covariates (V0, V1, V2 etc. in the phenotype data cov.tb) I am only intereste ...
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... I just summarized a dataset using the expresso() function. I then normalized the data using limma's "normalizebetweenarrays()" function. But now I need to pull out just the miRNA data from everying else on the chip...and while i have a list of miRNA transcript names, I have rownames such as "14qI-8_ ...
written 22 days ago by
RNAseqer • 110
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... Hey I have an odd problem:
I was using the oligo package to do RMA on some affy miRNA microarray data. It seems that the oligo package combines mutiple probes into one expression value automatically during the normalization process. Thats been great.
Now I would like to do cyclic loess normali ...
written 4 weeks ago by
RNAseqer • 110
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... Hello all,
I need to compare the performance of RMA to mas5.0 normalization on some microarray data. This is not a matter of weighing the merits of rma against those of mas5, but rather seeing if a signal detected in rma normalized data is present when a different normalization technique, mas5.0 ...
written 5 weeks ago by
RNAseqer • 110
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... Thanks! That is good to know. It seems as though this was fixed automatically a step or two later in the pipeline by the rma function. After rma the rownames do appear to be probe IDs again.
...
written 7 weeks ago by
RNAseqer • 110
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I have some normalized microarray data in an object generated by the following commands:
> raw_data5 <- oligo::read.celfiles(filenames =
"VV51m.CEL",
"VV50m.CEL",
...)
...
written 7 weeks ago by
RNAseqer • 110
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... > raw_data3 <- oligo::read.celfiles(filenames =
"VV51m.CEL",
"VV50m.CEL",
...
)
...
written 7 weeks ago by
RNAseqer • 110
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... Hello everyone,
Has anyone had experience changing the rownames of the expressionset (the intensity matrix) for an affy expression-set object?
Somehow mine got changed from probe IDs to simple numbers (1 for the first probe, 2 for the second etc.) and I'd like to change them back.
> exp ...
written 7 weeks ago by
RNAseqer • 110
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... Hello all,
So I have some Affy microarray data for miRNAs and I'm wondering what normalization techniques to apply to it. As I understand it the challenges inherent in miRNA nomalization are, unlike mRNA:
1) the smaller number of miRNAs as opposed to mRNA means there is less to work with
2) t ...
written 7 weeks ago by
RNAseqer • 110
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... Hello Kevin,
I'ts been a many years since I did anything with principal components and over the past few months I've done a lot of brushing up on the subject but I'm just having a bit of trouble understanding what some of their values are in the above covariate analysis.
As I understand it PCA ...
written 8 weeks ago by
RNAseqer • 110
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