User: sherajilir

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sherajilir0
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Posts by sherajilir

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Comment: C: Deseq2 PCA Anlysis
... Thanks Michael, I cannot do that since i cannot process the raw files due to lack of computational power. I am relying on raw counts from TCGA extracted by TCGABiolinks. ...
written 5 weeks ago by sherajilir0
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Deseq2 PCA Anlysis
... Hello everyone. I am doing differential expression analysis for a TCGA data set. When i checked PCA separation, i got something like this, a matter i have seen in GSEA as well. Two tumor samples are not separated from the normal. https://drive.google.com/file/d/1UZh-FQdCw9biCv9AzlfCLAzxLV008cSi/ ...
deseq2 pca written 5 weeks ago by sherajilir0 • updated 5 weeks ago by Michael Love23k
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Comment: C: DESEQ2 Batch effect
... Sorry for writting separately but just came to my mind to use shrinkage with apeglm package and got this https://drive.google.com/file/d/1ygZ1n9J_3he0L5ecFRFRTIPJV6TRzmmE/view?usp=sharing Now i think the problem is solved, though your feedback would be highly valuable. Thanks again ...
written 5 weeks ago by sherajilir0
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Comment: C: DESEQ2 Batch effect
... Thank you Michael for your prompt response. I did normalization and i'm getting an MA plot like this https://drive.google.com/file/d/1QeCzKQcTR5A-Wx7kGU52MvhfEj-27eCH/view?usp=sharing Do you think its acceptable? I have doubts because its not aligned to zero. Thank you once again ...
written 5 weeks ago by sherajilir0
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Comment: C: Annotating protein sequences
... I did not quite understand! You have protein sequences in your hand and want to classify them according to domains? ...
written 5 weeks ago by sherajilir0
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DESEQ2 Batch effect
... Hello everyone, I am analyzing coad-tcga dataset and there are two sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink happens). Thanks! ...
deseq2 batch written 5 weeks ago by sherajilir0 • updated 5 weeks ago by Michael Love23k
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Comment: C: Different annotation obtained from hgu133a2.db and affymetrix annotation release
... Some functions just get outdated and replaced by better and more "universal" ones. Its really tough sometimes to keep up with all the changes happening, especially towards the end of the year! Select is awesome though ...
written 4 months ago by sherajilir0
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Answer: A: logfold shrinkage DESeq2
... Thank you Michael for the quick reply. Actually the shrinked lfc MA plot is something like this https://www.dropbox.com/s/hun8s44twzxw3g2/Shrinked%20lfc%20plot.tiff?dl=0 But i think i got the answer.   ...
written 4 months ago by sherajilir0
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logfold shrinkage DESeq2
... Hi everyone, I Did DESseq2 differential expression analysis for 180 samples from TCGA using HTSEQ raw counts. After following all the steps and normalizing for two factors i got the expressed data with lof2FC, pval and padj. Then i did log-fold shrinkage using the apeglm package and im getting diff ...
deseq2 written 4 months ago by sherajilir0

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