FBR Capital Markets has lowered its profit estimates of Microsoft Corp. (NASDAQ:MSFT), citing lower PC shipments.

The brokerage cut its second quarter pro forma earnings estimate by 2 cents to 80 cents a share and revenue view by $300 million to $21 billion. It also slashed its fiscal 2012 pro forma profit forecast by 7 cents to $2.76 a share and revenue estimate by $1.1 billion to $74.8 billion.

For the second quarter, Wall Street expects Microsoft to earn 76 cents a share on revenue of $20.94 billion, according to analysts polled by Thomson Reuters. For fiscal 2012, analysts expect earnings of $2.72 a share on revenue of $ 74.5 billion.

While both IDC and Gartner reduced their PC estimates in December to a 1 percent drop, given a more challenging IT environment and a more severe negative impact from Thailand, Microsoft believes these estimates are likely to decline for the December quarter and the negative impact could persist in the near term.

The floods in Thailand have been causing disruptions to the production of hard disk drives since October 2011, and this has started to negatively affect the PC supply chain (and IT hardware in general). This was a headwind in the December quarter and is expected to be a more serious concern in the March quarter, analyst David Hilal wrote in a note to clients.

Hilal, who has a market perform rating on Microsoft stock, now assumes PC shipment growth of 3 percent for fiscal 2012 and 11 percent for fiscal 2013, down from 11 percent and 12 percent, respectively.

Shares of Microsoft closed Friday's regular trading session at $28.25 on Nasdaq, while Hilal has a price target of $28.