User: sherajilir

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sherajilir0
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Posts by sherajilir

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Microarray Data Analysis CDF Problem
... Thanks a lot Guido, it worked finally! ...
written 6 days ago by sherajilir0
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Microarray Data Analysis CDF Problem
... Hello Everyone, I am trying to normalize a dataset GSE45220 based on hugene.1.1.st.v1 platform. However, when i try to do rma or gcrma normalization, i get an error about the missing cdf-file which does not work for the package anyway. #GSE45220 BiocManager::install("GEOquery") librar ...
microarray normalization written 7 days ago by sherajilir0 • updated 6 days ago by Guido Hooiveld2.5k
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Answer: A: Downloading HTSeq raw reads with TCGABiolinks
... Ok problem solved! Seems like the package has trouble of compatibility with R3.5.3. Updated to R3.6.0 and reinstalled the package. ...
written 26 days ago by sherajilir0
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Downloading HTSeq raw reads with TCGABiolinks
... Hello Everyone! I have been trying for a while to download BRCA RNASeq data using TCGAbiolinks package from bioconductor. I followed the protocol online and everything works perfectly till GDCprepare step, where i get an error. My code is as follows: #BRCA HT-Seq extraction with TCGAbiolinks ...
rnaseq tcgabiolinks written 4 weeks ago by sherajilir0
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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 4 months 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 4 months ago by sherajilir0 • updated 4 months ago by Michael Love24k
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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 4 months 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 4 months 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 4 months 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 4 months ago by sherajilir0 • updated 4 months ago by Michael Love24k

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